diff --git a/.Rprofile b/.Rprofile
index 5b36bc35..81b960f5 100644
--- a/.Rprofile
+++ b/.Rprofile
@@ -1,26 +1 @@
source("renv/activate.R")
-
-# Set the repos using the renv.lock file
-renv_json <- jsonlite::read_json("renv.lock")
-renv_r_repos <- renv_json$R$Repositories
-
-# Extract the names
-repo_names <- purrr::flatten_chr(
- purrr::map(renv_r_repos,
- ~ .x$Name)
-)
-
-# Extract the URLs
-repo_urls <- purrr::flatten_chr(
- purrr::map(renv_r_repos,
- ~ .x$URL)
-)
-
-# Set the repo names
-names(repo_urls) <- repo_names
-
-# Set the options
-options(repos = repo_urls)
-
-# Remove all these objects
-rm(renv_json, renv_r_repos, repo_names, repo_urls)
diff --git a/.github/workflows/build-docker.yml b/.github/workflows/build-docker.yml
index 13cfb828..22feafa8 100644
--- a/.github/workflows/build-docker.yml
+++ b/.github/workflows/build-docker.yml
@@ -19,16 +19,27 @@ on:
- renv.lock
- requirements.txt
- current-modules.json
+ - .github/workflows/build-docker.yml
-# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+env:
+ REGISTRY_IMAGE: ccdl/training_rstudio
jobs:
- # This workflow contains a single job called "build"
build:
- # The type of runner that the job will run on
- runs-on: ubuntu-latest
+ strategy:
+ fail-fast: false
+ matrix:
+ include:
+ - platform: linux/amd64
+ runner: ubuntu-latest
+ - platform: linux/arm64
+ runner: ubuntu-24.04-arm
+ runs-on: ${{ matrix.runner }}
- # Steps represent a sequence of tasks that will be executed as part of the job
steps:
+ - name: Prepare env variables
+ run: |
+ platform=${{ matrix.platform }}
+ echo "PLATFORM_PAIR=${platform//\//-}" >> $GITHUB_ENV
- name: Check out the repo
uses: actions/checkout@v5
@@ -36,7 +47,7 @@ jobs:
if: startsWith(github.ref, 'refs/tags/')
run: |
GIT_TAG=${GITHUB_REF#refs/tags/}
- MODULES_TAG=$(jq -r '.release-tag' current-modules.json)
+ MODULES_TAG=$(jq -r '."release-tag"' current-modules.json)
if [ "$GIT_TAG" != "$MODULES_TAG" ]; then
echo "Error: current-modules.json release-tag ($MODULES_TAG) does not match git tag ($GIT_TAG)"
echo "Please update release-tag in current-modules.json to match the git tag (and modules, if needed), then update the GitHub release accordingly."
@@ -44,23 +55,22 @@ jobs:
fi
- name: Load 1Password secrets
- uses: 1password/load-secrets-action@v2
+ uses: 1password/load-secrets-action@v3
with:
export-env: true
env:
OP_SERVICE_ACCOUNT_TOKEN: ${{ secrets.TRAINING_OP_SERVICE_ACCOUNT_TOKEN }}
DOCKER_USER: ${{ secrets.OP_DOCKER_USERNAME }}
DOCKER_PASSWORD: ${{ secrets.OP_DOCKER_PASSWORD }}
- ACTION_MONITORING_SLACK: ${{ secrets.OP_ACTION_MONITORING_SLACK }}
- # Login to Dockerhub
- name: Login to DockerHub
uses: docker/login-action@v3
with:
username: ${{ env.DOCKER_USER }}
password: ${{ env.DOCKER_PASSWORD }}
- # set up Docker build
+ - name: Set up QEMU
+ uses: docker/setup-qemu-action@v3
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v3
@@ -68,7 +78,74 @@ jobs:
id: meta
uses: docker/metadata-action@v5
with:
- images: ccdl/training_rstudio
+ images: ${{ env.REGISTRY_IMAGE }}
+
+ # Build Docker image, push only on push events
+ - name: Build Docker image
+ id: build
+ uses: docker/build-push-action@v6
+ with:
+ push: ${{ github.event_name == 'push' }}
+ platforms: ${{ matrix.platform }}
+ outputs: type=image,push-by-digest=true,name-canonical=true
+ labels: ${{ steps.meta.outputs.labels }}
+ tags: ${{ env.REGISTRY_IMAGE }}
+ cache-from: type=registry,ref=${{ env.REGISTRY_IMAGE }}:buildcache-${{ env.PLATFORM_PAIR }}
+ cache-to: type=registry,ref=${{ env.REGISTRY_IMAGE }}:buildcache-${{ env.PLATFORM_PAIR }},mode=max
+
+ - name: Export digest
+ if: github.event_name == 'push'
+ run: |
+ mkdir -p ${{ runner.temp }}/digests
+ digest="${{ steps.build.outputs.digest }}"
+ touch "${{ runner.temp }}/digests/${digest#sha256:}"
+
+ - name: Upload digest
+ if: github.event_name == 'push'
+ uses: actions/upload-artifact@v4
+ with:
+ name: digests-${{ env.PLATFORM_PAIR }}
+ path: ${{ runner.temp }}/digests/*
+ if-no-files-found: error
+ retention-days: 1
+
+ merge:
+ runs-on: ubuntu-latest
+ needs:
+ - build
+ # only merge the manifests and push on push events
+ if: github.event_name == 'push'
+ steps:
+ - name: Load 1Password secrets
+ uses: 1password/load-secrets-action@v3
+ with:
+ export-env: true
+ env:
+ OP_SERVICE_ACCOUNT_TOKEN: ${{ secrets.TRAINING_OP_SERVICE_ACCOUNT_TOKEN }}
+ DOCKER_USER: ${{ secrets.OP_DOCKER_USERNAME }}
+ DOCKER_PASSWORD: ${{ secrets.OP_DOCKER_PASSWORD }}
+ ACTION_MONITORING_SLACK: ${{ secrets.OP_ACTION_MONITORING_SLACK }}
+
+ - name: Download digests
+ uses: actions/download-artifact@v4
+ with:
+ path: ${{ runner.temp }}/digests
+ pattern: digests-*
+ merge-multiple: true
+ - name: Login to DockerHub
+ uses: docker/login-action@v3
+ with:
+ username: ${{ env.DOCKER_USER }}
+ password: ${{ env.DOCKER_PASSWORD }}
+
+ - name: Set up Docker Buildx
+ uses: docker/setup-buildx-action@v3
+
+ - name: Docker meta
+ id: meta
+ uses: docker/metadata-action@v5
+ with:
+ images: ${{ env.REGISTRY_IMAGE }}
# each github tag will create a matching tag on dockerhub,
# with the most recent given the "latest" tag
# the most recent push to master will get an "edge" tag
@@ -76,18 +153,19 @@ jobs:
type=ref,event=tag
type=edge,branch=master
- # Build Docker image, push only on push events
- - name: Build Docker image
- uses: docker/build-push-action@v5
- with:
- push: ${{ github.event_name == 'push' }}
- tags: ${{ steps.meta.outputs.tags }}
- cache-from: type=registry,ref=ccdl/training_rstudio:buildcache
- cache-to: type=registry,ref=ccdl/training_rstudio:buildcache,mode=max
+ - name: Create manifest list and push
+ working-directory: ${{ runner.temp }}/digests
+ run: |
+ docker buildx imagetools create $(jq -cr '.tags | map("-t " + .) | join(" ")' <<< "$DOCKER_METADATA_OUTPUT_JSON") \
+ $(printf '${{ env.REGISTRY_IMAGE }}@sha256:%s ' *)
+
+ - name: Inspect image
+ run: |
+ docker buildx imagetools inspect ${{ env.REGISTRY_IMAGE }}:${{ steps.meta.outputs.version }}
# If we have a failure, Slack us
- name: Report failure to Slack
- if: ${{ github.event_name == 'push' }}
+ if: ${{ failure() }}
uses: ravsamhq/notify-slack-action@v2
with:
status: ${{ job.status }}
diff --git a/.github/workflows/make-live.yml b/.github/workflows/make-live.yml
index d10d0a2c..c37b4f6f 100644
--- a/.github/workflows/make-live.yml
+++ b/.github/workflows/make-live.yml
@@ -14,20 +14,22 @@ jobs:
make-live:
# The type of runner that the job will run on
runs-on: ubuntu-latest
- container:
- image: ccdl/training_rstudio:edge
steps:
+ - name: Free disk space
+ run: |
+ sudo rm -rf /usr/local/lib/android
+ sudo rm -rf /usr/share/dotnet
+ sudo rm -rf /opt/ghc
+ sudo rm -rf /usr/local/share/boost
+ sudo rm -rf "$AGENT_TOOLSDIRECTORY"
+ # Print free disk space
+ df -h
+
# Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
- name: Checkout code
uses: actions/checkout@v4
- - name: Configure git
- run: |
- git config --global --add safe.directory "$GITHUB_WORKSPACE"
- git config --local user.email "actions@github.com"
- git config --local user.name "GitHub Actions"
-
- name: Load 1Password secrets
uses: 1password/load-secrets-action@v2
with:
@@ -43,15 +45,26 @@ jobs:
env:
AWS_DEFAULT_REGION: us-east-1
run: |
- aws s3 sync s3://ccdl-training-data/training-modules/ .
+ aws s3 sync s3://ccdl-training-data/training-modules/ . --no-progress
+
+ - name: Pull latest Docker image
+ run: |
+ docker pull ccdl/training_rstudio:edge
- name: Render notebooks
env:
RENDER_RMD: ${{ github.event.inputs.rendering }}
- run: bash scripts/render-live.sh
+ run: |
+ docker run --rm \
+ --mount type=bind,source="$GITHUB_WORKSPACE",target=/training-modules \
+ -w /training-modules \
+ -e RENDER_RMD \
+ ccdl/training_rstudio:edge \
+ bash scripts/render-live.sh
# Make changes to pull request here
- name: Create PR with rendered notebooks
+ id: cpr
uses: peter-evans/create-pull-request@v6
with:
token: ${{ env.DOCS_BOT_GITHUB_TOKEN }}
diff --git a/.github/workflows/render-rmds.yml b/.github/workflows/render-rmds.yml
index 3b3cd56c..14271387 100644
--- a/.github/workflows/render-rmds.yml
+++ b/.github/workflows/render-rmds.yml
@@ -6,20 +6,29 @@ on:
branches:
- master
paths:
- - '**.Rmd'
- - '!**-live.Rmd' # don't trigger for live-only changes
- - '!**/exercise*.Rmd' # or exercise notebooks
- - '!**/setup/**.Rmd' # or setup notebooks
- - 'scripts/make-live.R'
- - 'scripts/render-live.sh'
+ - ".github/workflows/render-rmds.yml"
+ - "**.Rmd"
+ - "!**-live.Rmd" # don't trigger for live-only changes
+ - "!**/exercise*.Rmd" # or exercise notebooks
+ - "!**/setup/**.Rmd" # or setup notebooks
+ - "scripts/make-live.R"
+ - "scripts/render-live.sh"
jobs:
test-render:
runs-on: ubuntu-latest
- container:
- image: ccdl/training_rstudio:edge
steps:
+ - name: Free disk space
+ run: |
+ sudo rm -rf /usr/local/lib/android
+ sudo rm -rf /usr/share/dotnet
+ sudo rm -rf /opt/ghc
+ sudo rm -rf /usr/local/share/boost
+ sudo rm -rf "$AGENT_TOOLSDIRECTORY"
+ # Print free disk space
+ df -h
+
- name: Checkout code
uses: actions/checkout@v4
@@ -36,8 +45,16 @@ jobs:
env:
AWS_DEFAULT_REGION: us-east-1
run: |
- aws s3 sync s3://ccdl-training-data/training-modules/ .
+ aws s3 sync s3://ccdl-training-data/training-modules/ . --no-progress
+ - name: Pull latest Docker image
+ run: |
+ docker pull ccdl/training_rstudio:edge
- name: Render notebooks
- run: bash scripts/render-live.sh
+ run: |
+ docker run --rm \
+ --mount type=bind,source="$GITHUB_WORKSPACE",target=/training-modules \
+ -w /training-modules \
+ ccdl/training_rstudio:edge \
+ bash scripts/render-live.sh
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 15b2b996..34b25a16 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -215,7 +215,7 @@ In practice, this means that you will not need to add individual R packages to t
To use the Docker image for development, pull from Docker Hub with:
```
-docker pull --platform linux/amd64 ccdl/training_rstudio:edge
+docker pull ccdl/training_rstudio:edge
```
To run the container and mount a local volume, use the following from the root of this repository:
diff --git a/Dockerfile b/Dockerfile
index e551636f..9d08dc91 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,5 +1,6 @@
# Build salmon from source in a separate image
-FROM ubuntu:22.04 AS build
+# matching base image from https://github.com/rocker-org/rocker-versioned2/blob/master/dockerfiles/r-ver_4.5.2.Dockerfile
+FROM docker.io/library/ubuntu:noble AS build
# Build dependencies
RUN apt-get update -qq
@@ -15,6 +16,7 @@ RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
libdeflate-dev \
libisal-dev \
liblzma-dev \
+ libzstd-dev \
make \
pkg-config \
unzip \
@@ -29,7 +31,7 @@ RUN unzip awscliv2.zip
RUN ./aws/install
# Build salmon
-ARG SALMON_VERSION=1.10.1
+ARG SALMON_VERSION=1.10.3
RUN curl -LO https://github.com/COMBINE-lab/salmon/archive/refs/tags/v${SALMON_VERSION}.tar.gz
RUN tar xzf v${SALMON_VERSION}.tar.gz
RUN mkdir salmon-${SALMON_VERSION}/build
@@ -45,12 +47,12 @@ RUN cd fastp-${FASTP_VERSION} && \
make && make install
# Main image with Biocconductor and other tools
-FROM bioconductor/bioconductor_docker:3.19 AS final
+FROM bioconductor/bioconductor_docker:3.22 AS final
LABEL maintainer="ccdl@alexslemonade.org"
WORKDIR /rocker-build/
-# Additonal dependencies for AWS runtime
+# Additional dependencies for AWS runtime
RUN apt-get update -qq
RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
glibc-source \
@@ -66,21 +68,19 @@ RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
# Python packages
COPY requirements.txt requirements.txt
-RUN pip install -r requirements.txt
+RUN pip install -r requirements.txt --break-system-packages
# Use renv for R packages
WORKDIR /usr/local/renv
ENV RENV_CONFIG_CACHE_ENABLED=FALSE
RUN Rscript -e "install.packages('renv')"
-# Temporary fix for broken(?) RSamtools package
-RUN Rscript -e "install.packages('BiocManager'); BiocManager::install('Rsamtools')"
COPY renv.lock renv.lock
-RUN Rscript -e "renv::restore()" \
- rm -rf ~/.cache/R/renv && \
- rm -rf /tmp/downloaded_packages && \
- rm -rf /tmp/Rtmp*
+RUN Rscript -e "options(pkgType='binary'); renv::restore(repos = c(CRAN = 'https://packagemanager.posit.co/cran/__linux__/noble/latest'))" \
+ && rm -rf ~/.cache/R/renv \
+ && rm -rf /tmp/downloaded_packages \
+ && rm -rf /tmp/Rtmp*
# copy aws, salmon, and fastp binaries from the build image
COPY --from=build /usr/local/aws-cli/ /usr/local/aws-cli/
diff --git a/RNA-seq/01-qc_trim_quant.Rmd b/RNA-seq/01-qc_trim_quant.Rmd
index aa6ca7ac..f5299c1c 100644
--- a/RNA-seq/01-qc_trim_quant.Rmd
+++ b/RNA-seq/01-qc_trim_quant.Rmd
@@ -247,7 +247,7 @@ The index we used was built with `-k 23` and can be found here:
index/Homo_sapiens/short_index
```
-Using a smaller value for _k_ than the default (_k_ = 31) is appropriate for shorter reads and may improve sensitivity when using `--validateMappings` according to the [Salmon documentation](https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode).
+Using a smaller value for _k_ than the default (_k_ = 31) is appropriate for shorter reads and may improve sensitivity when using `--validateMappings` according to the [Salmon documentation](https://salmon.readthedocs.io/en/latest/salmon.html#salmon).
#### `-l`
@@ -285,5 +285,5 @@ The `--threads` argument controls the number of threads that are available to Sa
This in essence controls how much of the mapping can occur in parallel.
If you had access to a computer with many cores, you could increase the number of threads to make quantification go faster.
-**Navigate to** `data/gastric-cancer/salmon_quant/SRR585571/aux_info` **and open** `meta_info.json`**.
+**Navigate to** `data/gastric-cancer/salmon_quant/SRR585570/aux_info` **and open** `meta_info.json`**.
Look for a field called** `percent_mapped` **-- what value does this sample have?**
diff --git a/RNA-seq/02-gastric_cancer_tximeta.Rmd b/RNA-seq/02-gastric_cancer_tximeta.Rmd
index 0738a6c5..a8fe752e 100644
--- a/RNA-seq/02-gastric_cancer_tximeta.Rmd
+++ b/RNA-seq/02-gastric_cancer_tximeta.Rmd
@@ -120,24 +120,24 @@ sample_meta_df <- readr::read_tsv(meta_file)
sample_meta_df
```
-We'll want this information to be added to the `coldata`, which we can do by using a join function to match up the rows between the two data frames and combine them.
+We'll want this information to be added to the `coldata`, which we can do by using a join function to match up the rows between the two data frames and combine them to create a new data frame `coldata_joined`.
```{r join-sample_meta_df}
-coldata <- coldata |>
+coldata_joined <- coldata |>
dplyr::inner_join(sample_meta_df, by = c("names" = "srr_accession"))
-coldata
+coldata_joined
```
## Import expression data with `tximeta`
-Using the `coldata` data frame that we set up, we can now run the `tximeta()` to import our expression data while automatically finding and associating the transcript annotations that were used when we performed the quantification.
+Using the `coldata_joined` data frame that we set up, we can now run the `tximeta()` to import our expression data while automatically finding and associating the transcript annotations that were used when we performed the quantification.
The first time you run `tximeta()` you may get a message about storing downloaded transcriptome data in a cache directory so that it can retrieve the data more quickly the next time.
We recommend you use the cache, and accept the default location.
```{r tximeta, live = TRUE}
-txi_data <- tximeta(coldata)
+txi_data <- tximeta(coldata_joined)
```
*tximeta currently works easily for most human and mouse datasets, but requires a [few more steps for other species](https://bioconductor.org/packages/release/bioc/vignettes/tximeta/inst/doc/tximeta.html#What_if_checksum_isn%E2%80%99t_known).
diff --git a/RNA-seq/02-gastric_cancer_tximeta.nb.html b/RNA-seq/02-gastric_cancer_tximeta.nb.html
index 99d9795d..ce6fa77e 100644
--- a/RNA-seq/02-gastric_cancer_tximeta.nb.html
+++ b/RNA-seq/02-gastric_cancer_tximeta.nb.html
@@ -3264,8 +3264,8 @@
Summarize to gene
# Summarize to the gene level
gene_summarized <- summarizeToGene(txi_data)
-
-loading existing EnsDb created: 2025-07-16 21:08:01
+
+loading existing EnsDb created: 2025-11-20 20:30:47
obtaining transcript-to-gene mapping from database
diff --git a/components/dependencies.R b/components/dependencies.R
index fe381a4e..358fe6d8 100644
--- a/components/dependencies.R
+++ b/components/dependencies.R
@@ -36,3 +36,6 @@ library(scDblFinder)
# Loom file format functions for Single Cell data
library(LoomExperiment)
+
+# Needed for SingleR to run de with wilcox, for cell type exercises
+library(scrapper)
diff --git a/components/dictionary.txt b/components/dictionary.txt
index b6fadbe6..0387b616 100644
--- a/components/dictionary.txt
+++ b/components/dictionary.txt
@@ -1,5 +1,6 @@
ʹ
⚠️
+µm
Adelie
ADT
ADTs
@@ -15,6 +16,7 @@ AllCells
ALSF
Amezquita
AML
+anaplastic
Anders
Angerer
AnnotationDbi
@@ -46,6 +48,8 @@ biomolecular
bioRxiv
biospecimen
Blasi
+blastema
+blastemal
BMC
Bonferroni
bp
@@ -110,6 +114,7 @@ dplyr
dropdown
DropSeq
dumpFeatures
+ECM
effector
eigengene
embeddings
@@ -145,6 +150,7 @@ FCS
FDR
fgsea
fibrotic
+fiducials
Figshare
FLI
FN
@@ -191,6 +197,7 @@ hematopoietic
Hemberg
hexamer
Hippen
+histologic
histologies
Hm
Homebrew
@@ -314,6 +321,7 @@ Novia
NPC
NRAS
NRASG
+num
octothorps
OkabeIto
oligodendrocyte
@@ -343,6 +351,7 @@ pDC
PDX
ped
permalink
+permeabilized
phenotypes
Phred
Picelli
@@ -390,6 +399,7 @@ rmd
Rmd
RMS
roadmap
+roxygen
RPKMs
rRNA
Rscript
@@ -490,6 +500,7 @@ vectorization
vectorized
versicolor
virginica
+Visium
vitro
VST
Wattenberg
diff --git a/current-modules.json b/current-modules.json
index bb8d68be..fe8c34c7 100644
--- a/current-modules.json
+++ b/current-modules.json
@@ -1,5 +1,5 @@
{
- "release-tag": "2025-dev",
+ "release-tag": "2025-december",
"modules": ["scRNA-seq-advanced"],
"reference-modules": ["scRNA-seq"]
}
diff --git a/intro-to-R-tidyverse/01-intro_to_base_R.Rmd b/intro-to-R-tidyverse/01-intro_to_base_R.Rmd
index 79a9ec9d..5240f597 100644
--- a/intro-to-R-tidyverse/01-intro_to_base_R.Rmd
+++ b/intro-to-R-tidyverse/01-intro_to_base_R.Rmd
@@ -418,13 +418,9 @@ question_values %in% values_1_to_20
_Data frames are one of the most useful tools for data analysis in R._
They are tables which consist of rows and columns, much like a _spreadsheet_.
Each column is a variable which behaves as a _vector_, and each row is an observation.
-We will begin our exploration with dataset of measurements from three penguin species measured, which we can find in the [`palmerpenguins` package](https://allisonhorst.github.io/palmerpenguins/).
-We'll talk more about packages soon!
-To use this dataset, we will load it from the `palmerpenguins` package using a `::` (more on this later) and assign it to a variable named `penguins` in our current environment.
-
-```{r penguin-library}
-penguins <- palmerpenguins::penguins
-```
+We will begin our exploration with dataset of measurements from three penguin species measured using the built-in R dataset `penguins`.
+(This dataset was added as a built-in dataset to R version `4.5.0`;
+if you are working with an earlier version of R, it is available via the [`palmerpenguins` package](https://allisonhorst.github.io/palmerpenguins/) - we'll talk more about packages soon!)
 Artwork by [@allison_horst](https://twitter.com/allison_horst)
@@ -456,32 +452,33 @@ This provides a short view of the **str**ucture and contents of the data frame.
str(penguins)
```
-You'll notice that the column `species` is a _factor_: This is a special type of character variable that represents distinct categories known as "levels".
-We have learned here that there are three levels in the `species` column: Adelie, Chinstrap, and Gentoo.
+You'll notice that the columns `species`, `island`, and `sex` are labelled as _factor_: This is a special type of character variable that represents distinct categories known as "levels".
+Other columns are labelled as _num_ for numeric (with decimals), or _int_ for integer (numeric without decimals).
+
We might want to explore individual columns of the data frame more in-depth.
We can examine individual columns using the dollar sign `$` to select one by name:
```{r penguins-subset}
-# Extract bill_length_mm as a vector
-penguins$bill_length_mm
+# Extract bill_len as a vector
+penguins$bill_len
# indexing operators can be used on these vectors too
-penguins$bill_length_mm[1:10]
+penguins$bill_len[1:10]
```
We can perform our regular vector operations on columns directly.
```{r penguins-col-mean, live = TRUE}
-# calculate the mean of the bill_length_mm column
-mean(penguins$bill_length_mm,
+# calculate the mean of the bill_len column
+mean(penguins$bill_len,
na.rm = TRUE) # remove missing values before calculating the mean
```
We can also calculate the full summary statistics for a single column directly.
```{r penguins-col-summary, live = TRUE}
-# show a summary of the bill_length_mm column
-summary(penguins$bill_length_mm)
+# show a summary of the bill_len column
+summary(penguins$bill_len)
```
Extract `species` as a vector and subset it to see a preview.
diff --git a/intro-to-R-tidyverse/02-intro_to_ggplot2.Rmd b/intro-to-R-tidyverse/02-intro_to_ggplot2.Rmd
index fbbd2ae0..0cb33754 100644
--- a/intro-to-R-tidyverse/02-intro_to_ggplot2.Rmd
+++ b/intro-to-R-tidyverse/02-intro_to_ggplot2.Rmd
@@ -32,8 +32,8 @@ We performed three sets of contrasts:
**More ggplot2 resources:**
- [ggplot2 website](https://ggplot2.tidyverse.org/)
+- [ggplot2 book](https://ggplot2-book.org/)
- [Handy cheatsheet for ggplot2 (pdf)](https://github.com/rstudio/cheatsheets/raw/main/data-visualization.pdf)
-- [_Data Visualization, A practical introduction_](https://socviz.co/)
- [Data visualization chapter of _R for Data Science_](https://r4ds.hadley.nz/data-visualize.html)
- [ggplot2 online tutorial](http://r-statistics.co/Complete-Ggplot2-Tutorial-Part1-With-R-Code.html)
diff --git a/intro-to-R-tidyverse/03-intro_to_tidyverse.Rmd b/intro-to-R-tidyverse/03-intro_to_tidyverse.Rmd
index b3d3d915..bc58746c 100644
--- a/intro-to-R-tidyverse/03-intro_to_tidyverse.Rmd
+++ b/intro-to-R-tidyverse/03-intro_to_tidyverse.Rmd
@@ -52,7 +52,8 @@ library(tidyverse)
Note that if we had not imported the tidyverse set of packages using `library()` like above, and we wanted to use a tidyverse function like `read_tsv()`, we would need to tell R what package to find this function in.
To do this, we would use `::` to tell R to load in this function from the `readr` package by using `readr::read_tsv()`.
You will see this `::` method of referencing libraries within packages throughout the course.
-We like to use it in part to remove any ambiguity in which version of a function we are using; it is not too uncommon for different packages to use the same name for very different functions!
+We like to use it in part to remove any ambiguity in which version of a function we are using, even if the package was imported; it is not too uncommon for different packages to use the same name for very different functions!
+We'll use `::` syntax for external functions throughout this notebook.
## Managing directories
@@ -92,6 +93,7 @@ But we've also seen that this function will throw an error if you try to create
A different option is to use the [`fs`](https://fs.r-lib.org/) package, which provides functions for you to interact with your computer's file system with a more consistent behavior than the base R functions.
One function from this package is `fs::dir_create()` (note that it has an _underscore_, not a period), and much like the base R `dir.create()`, it creates directories.
It has some other helpful features too:
+
- It will simply do nothing if that directory already exists; no errors, and nothing will get overwritten
- It allows creating _nested_ directories by default, i.e. in one call make directories inside of other directories
@@ -142,16 +144,15 @@ data_dir <- "data"
```
Although base R has functions to read in data files, the functions in the `readr` package (part of the tidyverse) are faster and more straightforward to use so we are going to use those here.
-Because the file we are reading in is a TSV (tab separated values) file we will be using the `read_tsv` function.
-There are analogous functions for CSV (comma separated values) files (`read_csv()`) and other files types.
+Because the file we are reading in is a TSV (tab separated values) file we will be using the `readr::read_tsv()` function.
+There are analogous functions for CSV (comma separated values) files (`readr::read_csv()`) and other files types.
## Read in the differential expression analysis results file
```{r read-results}
stats_df <- readr::read_tsv(
- file.path(data_dir,
- "gene_results_GSE44971.tsv")
- )
+ file.path(data_dir, "gene_results_GSE44971.tsv")
+)
```
Following the template of the previous chunk, use this chunk to read in the file `GSE44971.tsv` that is in the `data` folder and save it in the variable `gene_df`.
@@ -159,9 +160,8 @@ Following the template of the previous chunk, use this chunk to read in the file
```{r read-expr, live = TRUE}
# Use this chunk to read in data from the file `GSE44971.tsv`
gene_df <- readr::read_tsv(
- file.path(data_dir,
- "GSE44971.tsv")
- )
+ file.path(data_dir, "GSE44971.tsv")
+)
```
Use this chunk to explore what `gene_df` looks like.
@@ -182,16 +182,18 @@ _Note:_ If you are using a version of `R` prior to 4.1 (or looking at older code
That pipe was the inspiration for the native R pipe we are using here.
While there are some minor differences, you can mostly treat them interchangeably as long as you load the `magrittr` package or `dplyr`, which also loads that version of the pipe.
-For example, the output from this:
+We'll being our journey into pipes using some core functions from the `dplyr` package (a core tidyverse package that offers "pliers" for your data).
+
+As our first example, the output from this:
```{r filter}
-filter(stats_df, contrast == "male_female")
+dplyr::filter(stats_df, contrast == "male_female")
```
...is the same as the output from this:
```{r filter-pipe}
-stats_df |> filter(contrast == "male_female")
+stats_df |> dplyr::filter(contrast == "male_female")
```
This can make your code cleaner and easier to follow a series of related commands.
@@ -200,9 +202,9 @@ Let's look at an example with our stats of of how the same functions look with o
*Example 1:* without pipes:
```{r steps-nopipe}
-stats_arranged <- arrange(stats_df, t_statistic)
-stats_filtered <- filter(stats_arranged, avg_expression > 50)
-stats_nopipe <- select(stats_filtered, contrast, log_fold_change, p_value)
+stats_arranged <- dplyr::arrange(stats_df, t_statistic)
+stats_filtered <- dplyr::filter(stats_arranged, avg_expression > 50)
+stats_nopipe <- dplyr::select(stats_filtered, contrast, log_fold_change, p_value)
```
UGH, we have to keep track of all of those different intermediate data frames and type their names so many times here!
@@ -213,15 +215,15 @@ It's annoying and makes it harder for people to read.
```{r steps-pipe, live = TRUE}
# Example of the same modifications as above but with pipes!
-stats_pipe <- stats_df |>
- arrange(t_statistic) |>
- filter(avg_expression > 50) |>
- select(contrast, log_fold_change, p_value)
+stats_pipe <- stats_df |>
+ dplyr::arrange(t_statistic) |>
+ dplyr::filter(avg_expression > 50) |>
+ dplyr::select(contrast, log_fold_change, p_value)
```
What the `|>` (pipe) is doing here is feeding the result of the expression on its left into the first argument of the next function (to its right, or on the next line here).
We can then skip that first argument (the data in these cases), and move right on to the part we care about at that step: what we are arranging, filtering, or selecting in this case.
-The key insight that makes the pipe work here is to recognize that each of these functions (`arrange`, `filter`, and `select`) are fundamental `dplyr` (a tidyverse package) functions which work as "data in, data out."
+The key insight that makes the pipe work here is to recognize that each of these functions (`dplyr::arrange`, `dplyr::filter`, and `dplyr::select`) are fundamental `dplyr` functions which work as "data in, data out."
In other words, these functions operate on data frames, and return data frames; you give them a data frame, and they give you back a data frame.
Because these functions all follow a "data in, data out" framework, we can chain them together with pipe and send data all the way through the...pipeline!
@@ -239,12 +241,12 @@ Now that hopefully you are convinced that the tidyverse can help you make your c
## Common tidyverse functions
Let's say we wanted to filter this gene expression dataset to particular sample groups.
-In order to do this, we would use the function `filter()` as well as a logic statement (usually one that refers to a column or columns in the data frame).
+In order to do this, we would use the function `dplyr::filter()` as well as a logic statement (usually one that refers to a column or columns in the data frame).
```{r filter-gene}
# Here let's filter stats_df to only keep the gene_symbol "SNCA"
stats_df |>
- filter(gene_symbol == "SNCA")
+ dplyr::filter(gene_symbol == "SNCA")
```
We can use `filter()` similarly for numeric statements.
@@ -252,7 +254,7 @@ We can use `filter()` similarly for numeric statements.
```{r filter-numeric, live = TRUE}
# Here let's filter the data to rows with average expression values above 50
stats_df |>
- filter(avg_expression > 50)
+ dplyr::filter(avg_expression > 50)
```
We can apply multiple filters at once, which will require all of them to be satisfied for every row in the results:
@@ -260,8 +262,10 @@ We can apply multiple filters at once, which will require all of them to be sati
```{r filter-2, live = TRUE}
# filter to highly expressed genes with contrast "male_female"
stats_df |>
- filter(contrast == "male_female",
- avg_expression > 50)
+ dplyr::filter(
+ contrast == "male_female",
+ avg_expression > 50
+ )
```
When we are filtering, the `%in%` operator can come in handy if we have multiple items we would like to match.
@@ -278,7 +282,7 @@ stats_df$gene_symbol %in% genes_of_interest
```{r filter-in, live = TRUE}
# filter to keep only genes of interest
stats_df |>
- filter(gene_symbol %in% c("SNCA", "CDKN1A"))
+ dplyr::filter(gene_symbol %in% c("SNCA", "CDKN1A"))
```
Let's return to our first `filter()` and build on to it.
@@ -290,9 +294,11 @@ Let's also save this as a new data frame called `stats_filtered_df`.
# filter to highly expressed "male_female"
# and select gene_symbol, log_fold_change and t_statistic
stats_filtered_df <- stats_df |>
- filter(contrast == "male_female",
- avg_expression > 50) |>
- select(log_fold_change, t_statistic)
+ dplyr::filter(
+ contrast == "male_female",
+ avg_expression > 50
+ ) |>
+ dplyr::select(log_fold_change, t_statistic)
```
Let's say we wanted to arrange this dataset so that the genes are arranged by the smallest p values to the largest.
@@ -300,7 +306,7 @@ In order to do this, we would use the function `arrange()` as well as the column
```{r arrange}
stats_df |>
- arrange(p_value)
+ dplyr::arrange(p_value)
```
What if we want to sort from largest to smallest?
@@ -310,15 +316,15 @@ We can use the same function, but instead use the `desc()` function and now we a
```{r arrange-desc}
# arrange descending by avg_expression
stats_df |>
- arrange(desc(avg_expression))
+ dplyr::arrange(desc(avg_expression))
```
What if we would like to create a new column of values?
-For that we use `mutate()` function.
+For that we use `dplyr::mutate()` function.
```{r mutate}
stats_df |>
- mutate(log10_p_value = -log10(p_value))
+ dplyr::mutate(log10_p_value = -log10(p_value))
```
What if we want to obtain summary statistics for a column or columns?
@@ -327,19 +333,26 @@ Here we will use summarize to calculate two summary statistics of log-fold chang
```{r summarize}
stats_df |>
- summarize(mean(log_fold_change),
- sd(log_fold_change))
+ dplyr::summarize(
+ # name the columns mean_lfc an sd_lfc
+ mean_lfc = mean(log_fold_change),
+ sd_lfc = sd(log_fold_change)
+ )
```
What if we'd like to obtain a summary statistics but have them for various groups?
Conveniently named, there's a function called `group_by()` that seamlessly allows us to do this.
Also note that `group_by()` allows us to group by multiple variables at a time if you want to.
+We'll use this function to create a grouped summary data frame and save it to a variable `stats_summary_df`.
+
```{r summarize-groups, live = TRUE}
stats_summary_df <- stats_df |>
- group_by(contrast) |>
- summarize(mean(log_fold_change),
- sd(log_fold_change))
+ dplyr::group_by(contrast) |>
+ dplyr::summarize(
+ mean_lfc = mean(log_fold_change),
+ sd_lfc = sd(log_fold_change)
+ )
```
Let's look at a preview of what we made:
@@ -454,7 +467,7 @@ In this case we want to match the gene information between the two, so we will s
stats_df |>
# Join based on their shared column
# Called ensembl_id in stats_df and called Gene in gene_df
- inner_join(gene_df, by = c('ensembl_id' = 'Gene'))
+ dplyr::inner_join(gene_df, by = c('ensembl_id' = 'Gene'))
```
## Save data to files
diff --git a/pathway-analysis/01-overrepresentation_analysis.Rmd b/pathway-analysis/01-overrepresentation_analysis.Rmd
index 8e7a62f1..afc79f52 100644
--- a/pathway-analysis/01-overrepresentation_analysis.Rmd
+++ b/pathway-analysis/01-overrepresentation_analysis.Rmd
@@ -59,9 +59,7 @@ library(org.Mm.eg.db)
# We'll create a directory to specifically hold the ORA results if it doesn't
# exist yet
results_dir <- file.path("results", "leukemia")
-if (!dir.exists(results_dir)) {
- dir.create(results_dir, recursive = TRUE)
-}
+fs::dir_create(results_dir)
```
#### Input files
@@ -107,7 +105,7 @@ The results we're interested in here come from mouse samples, so we can obtain j
mm_msigdb_df <- msigdbr(species = "Mus musculus")
```
-MSigDB contains 8 different gene set collections.
+MSigDB contains 9 different gene set collections.
H: hallmark gene sets
C1: positional gene sets
@@ -117,23 +115,26 @@ MSigDB contains 8 different gene set collections.
C5: GO gene sets
C6: oncogenic signatures
C7: immunologic signatures
+ C8: cell type signatures
In this example, we will use canonical pathways which are ([ref](https://www.gsea-msigdb.org/gsea/msigdb/collections.jsp)):
> Gene sets from pathway databases. Usually, these gene sets are canonical representations of a biological process compiled by domain experts.
And are a subset of `C2: curated gene sets`.
-Specifically, we will use the [KEGG (Kyoto Encyclopedia of Genes and Genomes)](https://www.genome.jp/kegg/) pathways.
+Specifically, we will use the [KEGG (Kyoto Encyclopedia of Genes and Genomes)](https://www.genome.jp/kegg/) pathways, which is denoted as `CP:KEGG_MEDICUS` in this version of `msigdbr`.
```{r filter_to_kegg}
# Filter the mouse data frame to the KEGG pathways that are included in the
# curated gene sets
mm_kegg_df <- mm_msigdb_df |>
- dplyr::filter(gs_cat == "C2", # curated gene sets
- gs_subcat == "CP:KEGG") # KEGG pathways
+ dplyr::filter(
+ gs_collection == "C2", # curated gene set
+ gs_subcollection == "CP:KEGG_MEDICUS" # KEGG pathways
+ )
```
-*Note: We could specified that we wanted the KEGG gene sets using the `category` and `subcategory` arguments of `msigdbr()`, but we're going for general steps!*
+*Note: We could specified that we wanted the KEGG gene sets using the `collection` and `subcollection` arguments of `msigdbr()`, but we're going for general steps!*
```{r mm_kegg_columns}
colnames(mm_kegg_df)
@@ -179,18 +180,20 @@ The function we will use to map from Ensembl gene IDs to gene symbols is called
```{r map_to_symbol}
# This returns a named vector which we can convert to a data frame, where
# the keys (Ensembl IDs) are the names
-symbols_vector <- mapIds(org.Mm.eg.db, # Specify the annotation package
- # The vector of gene identifiers we want to
- # map
- keys = vs_low_df$Gene,
- # What type of gene identifiers we're starting
- # with
- keytype = "ENSEMBL",
- # The type of gene identifier we want returned
- column = "SYMBOL",
- # In the case of 1:many mappings, return the
- # first one. This is default behavior!
- multiVals = "first")
+symbols_vector <- mapIds(
+ org.Mm.eg.db, # Specify the annotation package
+ # The vector of gene identifiers we want to
+ # map
+ keys = vs_low_df$Gene,
+ # What type of gene identifiers we're starting
+ # with
+ keytype = "ENSEMBL",
+ # The type of gene identifier we want returned
+ column = "SYMBOL",
+ # In the case of 1:many mappings, return the
+ # first one. This is default behavior!
+ multiVals = "first"
+)
# We would like a data frame we can join to the DGE results
symbols_df <- data.frame(
@@ -210,10 +213,12 @@ Let's do this first for the comparison to the low stem cell capacity population.
```{r add_symbols, live = TRUE}
vs_low_df <- symbols_df |>
# An *inner* join will only return rows that are in both data frames
- dplyr::inner_join(vs_low_df,
- # The name of the column that contains the Ensembl gene IDs
- # in the left data frame and right data frame
- by = c("ensembl_id" = "Gene"))
+ dplyr::inner_join(
+ vs_low_df,
+ # The name of the column that contains the Ensembl gene IDs
+ # in the left data frame and right data frame
+ by = c("ensembl_id" = "Gene")
+ )
```
### Drop `NA` values
@@ -226,7 +231,7 @@ This will also drop genes that have an Ensembl gene identifier but no gene symbo
```{r complete_cases}
# Remove rows that are not complete (e.g., contain NAs) by filtering to only
# complete rows
-vs_low_df <- vs_low_df |>
+vs_low_complete_df <- vs_low_df |>
tidyr::drop_na()
```
@@ -290,10 +295,12 @@ We'll start with the high stem cell capacity vs. low stem cell capacity populati
Genes with positive log2 fold-changes (LFC) will be more highly expressed in the high stem cell capacity cells based on how we set up the analysis.
```{r high_capacity_genes}
-vs_low_genes <- vs_low_df |>
+vs_low_genes <- vs_low_complete_df |>
# Filter to the positive LFC and filter based on significance too (padj)
- dplyr::filter(log2FoldChange > 0,
- padj < 0.05) |>
+ dplyr::filter(
+ log2FoldChange > 0,
+ padj < 0.05
+ ) |>
# Return a vector of gene symbols
dplyr::pull(gene_symbol)
```
@@ -306,8 +313,10 @@ Now, we'll take the same steps for our other results.
```{r unsorted_genes_to_remove, live = TRUE}
vs_unsorted_genes <- vs_unsorted_df |>
- dplyr::filter(log2FoldChange > 0,
- padj < 0.05) |>
+ dplyr::filter(
+ log2FoldChange > 0,
+ padj < 0.05
+ ) |>
dplyr::pull(gene_symbol)
```
@@ -335,8 +344,10 @@ We can use another function for set operations, `intersect()`, to get our backgr
```{r get_background_set}
# intersect() will return the genes in both sets - we are using the entire data
# frame here (complete cases), not just the significant genes
-background_set <- intersect(vs_low_df$gene_symbol,
- vs_unsorted_df$gene_symbol)
+background_set <- intersect(
+ vs_low_complete_df$gene_symbol,
+ vs_unsorted_df$gene_symbol
+)
# Remove anything that couldn't reliably be measured/assessed in both from the
# genes of interest list - using intersect() will drop anything in the first set
@@ -381,13 +392,13 @@ kegg_result_df <- data.frame(kegg_ora_results@result)
We can use a dot plot to visualize our significant enrichment results.
-```{r dotplot, live = TRUE}
+```{r dotplot, fig.width = 10, live = TRUE}
enrichplot::dotplot(kegg_ora_results)
```
We can use an [UpSet plot](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4720993/) to visualize the **overlap** between the gene sets that were returned as significant.
-```{r upsetplot, live = TRUE}
+```{r upsetplot, fig.width = 10, live = TRUE}
enrichplot::upsetplot(kegg_ora_results)
```
diff --git a/pathway-analysis/02-gene_set_enrichment_analysis.Rmd b/pathway-analysis/02-gene_set_enrichment_analysis.Rmd
index 3c79f68b..1d6dd544 100644
--- a/pathway-analysis/02-gene_set_enrichment_analysis.Rmd
+++ b/pathway-analysis/02-gene_set_enrichment_analysis.Rmd
@@ -52,6 +52,10 @@ library(clusterProfiler)
library(msigdbr)
```
+```{r set seed}
+set.seed(2020)
+```
+
### Directories and Files
#### Directories
@@ -63,9 +67,7 @@ input_dir <- file.path("..", "RNA-seq", "results", "NB-cell")
# We will create a directory to specifically hold our GSEA results if it does
# not yet exist
output_dir <- file.path("results", "NB-cell")
-if (!dir.exists(output_dir)) {
- dir.create(output_dir, recursive = TRUE)
-}
+fs::dir_create(output_dir)
```
#### Input files
@@ -119,11 +121,13 @@ We'll use the Hallmark collection for GSEA.
Notably, there are only 50 gene sets included in this collection.
The fewer gene sets we test, the lower our multiple hypothesis testing burden.
-We can retrieve only the Hallmark gene sets by specifying `category = "H"` to the `msigdbr()` function.
+We can retrieve only the Hallmark gene sets by specifying `collection = "H"` to the `msigdbr()` function.
```{r hallmark_sets, live = TRUE}
-hs_hallmark_df <- msigdbr(species = "Homo sapiens",
- category = "H")
+hs_hallmark_df <- msigdbr(
+ species = "Homo sapiens",
+ collection = "H"
+)
```
## Differential gene expression results
@@ -238,14 +242,18 @@ Now for the analysis!
We can use the `GSEA()` function to perform GSEA with any generic set of gene sets, but there are several functions for using specific, commonly used gene sets (e.g., `gseKEGG()`).
```{r run_gsea}
-gsea_results <- GSEA(geneList = lfc_vector, # ordered ranked gene list
- minGSSize = 25, # minimum gene set size
- maxGSSize = 500, # maximum gene set set
- pvalueCutoff = 0.05,
- pAdjustMethod = "BH", # correction for multiple hypothesis testing
- TERM2GENE = dplyr::select(hs_hallmark_df,
- gs_name,
- gene_symbol))
+gsea_results <- GSEA(
+ geneList = lfc_vector, # ordered ranked gene list
+ minGSSize = 25, # minimum gene set size
+ maxGSSize = 500, # maximum gene set set
+ pvalueCutoff = 0.05,
+ pAdjustMethod = "BH", # correction for multiple hypothesis testing
+ TERM2GENE = dplyr::select(
+ hs_hallmark_df,
+ gs_name,
+ gene_symbol
+ )
+)
```
The warning about ties means that there are multiple genes that have the same log2 fold change value.
diff --git a/pathway-analysis/03-gene_set_variation_analysis.Rmd b/pathway-analysis/03-gene_set_variation_analysis.Rmd
index abcbb998..6e8862c1 100644
--- a/pathway-analysis/03-gene_set_variation_analysis.Rmd
+++ b/pathway-analysis/03-gene_set_variation_analysis.Rmd
@@ -57,9 +57,7 @@ input_dir <- file.path("data", "open-pbta")
# Create a directory specifically for the results using this dataset
output_dir <- file.path("results", "open-pbta")
-if (!dir.exists(output_dir)) {
- dir.create(output_dir, recursive = TRUE)
-}
+fs::dir_create(output_dir)
```
#### Input
@@ -164,9 +162,7 @@ gsva_results <- gsva(
kcdf = "Gaussian",
# enrichment score is the difference between largest positive and negative
maxDiff = TRUE
- ),
- # Use 4 cores for multiprocessing
- BPPARAM = BiocParallel::MulticoreParam(4)
+ )
)
```
@@ -211,8 +207,9 @@ random_gene_sets <- rep(gene_set_size, nreps) |> # Repeat gene sizes so we run
purrr::map(
# Sample the vector of all genes, choosing the number of items specified
# in the element of gene set size
- ~ base::sample(x = all_genes,
- size = .x)
+ \(geneset_size) {
+ base::sample(x = all_genes, size = geneset_size)
+ }
)
```
@@ -224,9 +221,13 @@ The Hallmarks list we used earlier stored the gene set names as the name of the
# number
lengths_vector <- random_gene_sets |>
# Get the length of each gene set (number of genes)
- purrr::map(~ length(.x)) |>
+ purrr::map(length) |>
# Make it "pathway_"
- purrr::map(~ paste0("pathway_", .x)) |>
+ purrr::map(
+ \(geneset_size) {
+ paste0("pathway_", geneset_size)
+ }
+ ) |>
# Return a vector
purrr::flatten_chr()
@@ -247,9 +248,7 @@ random_gsva_results <- gsva(
maxSize = 500,
kcdf = "Gaussian",
maxDiff = TRUE
- ),
- # Use 4 cores for multiprocessing
- BPPARAM = BiocParallel::MulticoreParam(4)
+ )
)
```
diff --git a/renv.lock b/renv.lock
index 752ed02d..d6d0ab6b 100644
--- a/renv.lock
+++ b/renv.lock
@@ -1,2128 +1,5955 @@
{
"R": {
- "Version": "4.4.0",
+ "Version": "4.5.2",
"Repositories": [
{
"Name": "BioCsoft",
- "URL": "https://bioconductor.org/packages/3.19/bioc"
+ "URL": "https://bioconductor.org/packages/3.22/bioc"
},
{
"Name": "BioCann",
- "URL": "https://bioconductor.org/packages/3.19/data/annotation"
+ "URL": "https://bioconductor.org/packages/3.22/data/annotation"
},
{
"Name": "BioCexp",
- "URL": "https://bioconductor.org/packages/3.19/data/experiment"
+ "URL": "https://bioconductor.org/packages/3.22/data/experiment"
},
{
"Name": "BioCworkflows",
- "URL": "https://bioconductor.org/packages/3.19/workflows"
+ "URL": "https://bioconductor.org/packages/3.22/workflows"
},
{
"Name": "BioCbooks",
- "URL": "https://bioconductor.org/packages/3.19/books"
+ "URL": "https://bioconductor.org/packages/3.22/books"
},
{
"Name": "CRAN",
"URL": "https://p3m.dev/cran/latest"
+ },
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+ "Repository": "Bioconductor 3.22",
+ "Author": "Aaron Lun [aut], Jonathan Griffiths [ctb, cre], Davis McCarthy [ctb], Dongze He [ctb], Rob Patro [ctb]",
+ "Maintainer": "Jonathan Griffiths "
},
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"Package": "EnhancedVolcano",
- "Version": "1.22.0",
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"Source": "Bioconductor",
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+ "Authors@R": "c( person(\"Kevin\", \"Blighe\", role = c(\"aut\")), person(\"Jared\", \"Andrews\", email = \"jared.andrews07@gmail.com\", role = c(\"cre\", \"ctb\"), comment = c(ORCID = \"0000-0002-0780-6248\")), person(\"Sharmila\", \"Rana\", role = c(\"aut\")), person(\"Emir\", \"Turkes\", role = c(\"ctb\")), person(\"Benjamin\", \"Ostendorf\", role = c(\"ctb\")), person(\"Andrea\", \"Grioni\", role = c(\"ctb\")), person(\"Myles\", \"Lewis\", role = c(\"aut\")))",
+ "Maintainer": "Jared Andrews ",
+ "Description": "Volcano plots represent a useful way to visualise the results of differential expression analyses. Here, we present a highly-configurable function that produces publication-ready volcano plots. EnhancedVolcano will attempt to fit as many point labels in the plot window as possible, thus avoiding 'clogging' up the plot with labels that could not otherwise have been read. Other functionality allows the user to identify up to 4 different types of attributes in the same plot space via colour, shape, size, and shade parameter configurations.",
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+ "Encoding": "UTF-8",
+ "Depends": [
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+ "ggrepel"
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+ "Copyright": "ANN Copyright (c) 1997-2010 University of Maryland and Sunil Arya and David Mount. All Rights Reserved.",
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+ "Suggests": [
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+ "Description": "Cover-tree and kd-tree fast k-nearest neighbor search algorithms and related applications including KNN classification, regression and information measures are implemented.",
+ "License": "GPL (>= 2)",
+ "NeedsCompilation": "yes",
+ "Repository": "CRAN",
+ "Author": "Alina Beygelzimer [aut] (cover tree library), Sham Kakadet [aut] (cover tree library), John Langford [aut] (cover tree library), Sunil Arya [aut] (ANN library 1.1.2 for the kd-tree approach), David Mount [aut] (ANN library 1.1.2 for the kd-tree approach), Shengqiao Li [aut, cre]",
+ "Maintainer": "Shengqiao Li ",
+ "Encoding": "UTF-8"
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+ "Title": "Get data from NCBI Gene Expression Omnibus (GEO)",
+ "Date": "2025-09-03",
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+ "SingleCellExperiment"
+ ],
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+ "biocViews": "Microarray, DataImport, OneChannel, TwoChannel, SAGE",
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+ "Version": "2.4.0",
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+ "License": "GPL (>= 2.0)",
+ "URL": "https://ggobi.github.io/ggally/, https://github.com/ggobi/ggally",
+ "BugReports": "https://github.com/ggobi/ggally/issues",
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+ "Config/testthat/edition": "3",
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+ "Maintainer": "Guangchuang Yu ",
+ "Description": "The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R package for semantic similarity computation among GO terms, sets of GO terms, gene products and gene clusters. GOSemSim implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively.",
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},
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- "XML",
- "annotate",
- "graph",
- "methods"
+ "Type": "Package",
+ "Title": "Gene set enrichment data structures and methods",
+ "Authors@R": "c( person(\"Martin\", \"Morgan\", role = \"aut\"), person(\"Seth\", \"Falcon\", role = \"aut\"), person(\"Robert\", \"Gentleman\", role = \"aut\"), person(\"Paul\", \"Villafuerte\", role = \"ctb\", comment = \"'GSEABase' vignette translation from Sweave to Rmarkdown / HTML\"), person(\"Bioconductor Package Maintainer\", role = \"cre\", email = \"maintainer@bioconductor.org\" ))",
+ "Description": "This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA).",
+ "License": "Artistic-2.0",
+ "Depends": [
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+ "BiocGenerics (>= 0.13.8)",
+ "Biobase (>= 2.17.8)",
+ "annotate (>= 1.45.3)",
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+ "Maintainer": "Bioconductor Package Maintainer "
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- "GSEABase",
+ "Title": "Gene Set Variation Analysis for Microarray and RNA-Seq Data",
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"HDF5Array",
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+ "DelayedMatrixStats",
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+ "URL": "https://Matrix.R-forge.R-project.org",
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+ "Author": "Laurent Gatto , Johannes Rainer ",
+ "Maintainer": "Laurent Gatto ",
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+ "Authors@R": "c(person(\"Henrik\", \"Bengtsson\", role=c(\"aut\", \"cre\", \"cph\"), email = \"henrikb@braju.com\"))",
+ "Author": "Henrik Bengtsson [aut, cre, cph]",
+ "Maintainer": "Henrik Bengtsson ",
+ "Description": "Methods that simplify the setup of S3 generic functions and S3 methods. Major effort has been made in making definition of methods as simple as possible with a minimum of maintenance for package developers. For example, generic functions are created automatically, if missing, and naming conflict are automatically solved, if possible. The method setMethodS3() is a good start for those who in the future may want to migrate to S4. This is a cross-platform package implemented in pure R that generates standard S3 methods.",
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+ "LazyLoad": "TRUE",
+ "URL": "https://github.com/HenrikBengtsson/R.methodsS3",
+ "BugReports": "https://github.com/HenrikBengtsson/R.methodsS3/issues",
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+ "Title": "R Object-Oriented Programming with or without References",
+ "Authors@R": "c(person(\"Henrik\", \"Bengtsson\", role=c(\"aut\", \"cre\", \"cph\"), email = \"henrikb@braju.com\"))",
+ "Author": "Henrik Bengtsson [aut, cre, cph]",
+ "Maintainer": "Henrik Bengtsson ",
+ "Description": "Methods and classes for object-oriented programming in R with or without references. Large effort has been made on making definition of methods as simple as possible with a minimum of maintenance for package developers. The package has been developed since 2001 and is now considered very stable. This is a cross-platform package implemented in pure R that defines standard S3 classes without any tricks.",
+ "License": "LGPL (>= 2.1)",
+ "LazyLoad": "TRUE",
+ "URL": "https://henrikbengtsson.github.io/R.oo/, https://github.com/HenrikBengtsson/R.oo",
+ "BugReports": "https://github.com/HenrikBengtsson/R.oo/issues",
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+ "Version": "2.13.0",
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- "R.methodsS3",
- "R.oo",
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+ "R (>= 2.14.0)",
+ "R.oo"
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"tools",
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+ "R.methodsS3"
],
- "Hash": "3dc2829b790254bfba21e60965787651"
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+ "Title": "Various Programming Utilities",
+ "Authors@R": "c(person(\"Henrik\", \"Bengtsson\", role=c(\"aut\", \"cre\", \"cph\"), email = \"henrikb@braju.com\"))",
+ "Author": "Henrik Bengtsson [aut, cre, cph]",
+ "Maintainer": "Henrik Bengtsson ",
+ "Description": "Utility functions useful when programming and developing R packages.",
+ "License": "LGPL (>= 2.1)",
+ "LazyLoad": "TRUE",
+ "URL": "https://henrikbengtsson.github.io/R.utils/, https://github.com/HenrikBengtsson/R.utils",
+ "BugReports": "https://github.com/HenrikBengtsson/R.utils/issues",
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- "Hash": "470851b6d5d0ac559e9d01bb352b4021"
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+ "Title": "Encapsulated Classes with Reference Semantics",
+ "Authors@R": "c( person(\"Winston\", \"Chang\", , \"winston@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )",
+ "Description": "Creates classes with reference semantics, similar to R's built-in reference classes. Compared to reference classes, R6 classes are simpler and lighter-weight, and they are not built on S4 classes so they do not require the methods package. These classes allow public and private members, and they support inheritance, even when the classes are defined in different packages.",
+ "License": "MIT + file LICENSE",
+ "URL": "https://r6.r-lib.org, https://github.com/r-lib/R6",
+ "BugReports": "https://github.com/r-lib/R6/issues",
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+ "Maintainer": "Winston Chang ",
+ "Repository": "CRAN"
},
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"Version": "1.1-3",
"Source": "Repository",
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+ "Date": "2022-04-03",
+ "Title": "ColorBrewer Palettes",
+ "Authors@R": "c(person(given = \"Erich\", family = \"Neuwirth\", role = c(\"aut\", \"cre\"), email = \"erich.neuwirth@univie.ac.at\"))",
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+ "Description": "Provides color schemes for maps (and other graphics) designed by Cynthia Brewer as described at http://colorbrewer2.org.",
+ "License": "Apache License 2.0",
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+ "SystemRequirements": "GNU make, libcurl",
+ "Description": "A wrapper for 'libcurl' Provides functions to allow one to compose general HTTP requests and provides convenient functions to fetch URIs, get & post forms, etc. and process the results returned by the Web server. This provides a great deal of control over the HTTP/FTP/... connection and the form of the request while providing a higher-level interface than is available just using R socket connections. Additionally, the underlying implementation is robust and extensive, supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict, ldap, and also supports cookies, redirects, authentication, etc.",
+ "License": "BSD_3_clause + file LICENSE",
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"methods"
],
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+ "Source": "Repository",
+ "Title": "SQLite Interface for R",
+ "Date": "2026-02-05",
+ "Authors@R": "c( person(\"Kirill\", \"Müller\", , \"kirill@cynkra.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-1416-3412\")), person(\"Hadley\", \"Wickham\", role = \"aut\"), person(c(\"David\", \"A.\"), \"James\", role = \"aut\"), person(\"Seth\", \"Falcon\", role = \"aut\"), person(\"D. Richard\", \"Hipp\", role = \"ctb\", comment = \"for the included SQLite sources\"), person(\"Dan\", \"Kennedy\", role = \"ctb\", comment = \"for the included SQLite sources\"), person(\"Joe\", \"Mistachkin\", role = \"ctb\", comment = \"for the included SQLite sources\"), person(, \"SQLite Authors\", role = \"ctb\", comment = \"for the included SQLite sources\"), person(\"Liam\", \"Healy\", role = \"ctb\", comment = \"for the included SQLite sources\"), person(\"R Consortium\", role = \"fnd\"), person(, \"RStudio\", role = \"cph\") )",
+ "Description": "Embeds the SQLite database engine in R and provides an interface compliant with the DBI package. The source for the SQLite engine (version 3.51.2) and for various extensions is included. System libraries will never be consulted because this package relies on static linking for the plugins it includes; this also ensures a consistent experience across all installations.",
+ "License": "LGPL (>= 2.1)",
+ "URL": "https://rsqlite.r-dbi.org, https://github.com/r-dbi/RSQLite",
+ "BugReports": "https://github.com/r-dbi/RSQLite/issues",
+ "Depends": [
+ "R (>= 3.1.0)"
+ ],
+ "Imports": [
"bit64",
- "blob",
- "cpp11",
+ "blob (>= 1.2.0)",
+ "DBI (>= 1.2.0)",
"memoise",
"methods",
"pkgconfig",
- "plogr",
"rlang"
],
- "Hash": "ae4a925e0f6bb1b7e5fa96b739c5221a"
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+ "magrittr",
+ "rmarkdown",
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+ "xml2"
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+ "Config/Needs/website": "r-dbi/dbitemplate",
+ "Config/autostyle/scope": "line_breaks",
+ "Config/autostyle/strict": "false",
+ "Config/testthat/edition": "3",
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+ "NeedsCompilation": "yes",
+ "Author": "Kirill Müller [aut, cre] (ORCID: ), Hadley Wickham [aut], David A. James [aut], Seth Falcon [aut], D. Richard Hipp [ctb] (for the included SQLite sources), Dan Kennedy [ctb] (for the included SQLite sources), Joe Mistachkin [ctb] (for the included SQLite sources), SQLite Authors [ctb] (for the included SQLite sources), Liam Healy [ctb] (for the included SQLite sources), R Consortium [fnd], RStudio [cph]",
+ "Maintainer": "Kirill Müller ",
+ "Repository": "CRAN"
},
"RSpectra": {
"Package": "RSpectra",
- "Version": "0.16-1",
- "Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "Matrix",
- "R",
+ "Version": "0.16-2",
+ "Source": "Repository",
+ "Type": "Package",
+ "Title": "Solvers for Large-Scale Eigenvalue and SVD Problems",
+ "Date": "2024-07-18",
+ "Authors@R": "c( person(\"Yixuan\", \"Qiu\", , \"yixuan.qiu@cos.name\", c(\"aut\", \"cre\")), person(\"Jiali\", \"Mei\", , \"vermouthmjl@gmail.com\", \"aut\", comment = \"Function interface of matrix operation\"), person(\"Gael\", \"Guennebaud\", , \"gael.guennebaud@inria.fr\", \"ctb\", comment = \"Eigenvalue solvers from the 'Eigen' library\"), person(\"Jitse\", \"Niesen\", , \"jitse@maths.leeds.ac.uk\", \"ctb\", comment = \"Eigenvalue solvers from the 'Eigen' library\") )",
+ "Description": "R interface to the 'Spectra' library for large-scale eigenvalue and SVD problems. It is typically used to compute a few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues, which is usually more efficient than eigen() if k << n. This package provides the 'eigs()' function that does the similar job as in 'Matlab', 'Octave', 'Python SciPy' and 'Julia'. It also provides the 'svds()' function to calculate the largest k singular values and corresponding singular vectors of a real matrix. The matrix to be computed on can be dense, sparse, or in the form of an operator defined by the user.",
+ "License": "MPL (>= 2)",
+ "URL": "https://github.com/yixuan/RSpectra",
+ "BugReports": "https://github.com/yixuan/RSpectra/issues",
+ "Depends": [
+ "R (>= 3.0.2)"
+ ],
+ "Imports": [
+ "Matrix (>= 1.1-0)",
+ "Rcpp (>= 0.11.5)"
+ ],
+ "Suggests": [
+ "knitr",
+ "rmarkdown",
+ "prettydoc"
+ ],
+ "LinkingTo": [
"Rcpp",
- "RcppEigen"
+ "RcppEigen (>= 0.3.3.3.0)"
],
- "Hash": "6b5ab997fd5ff6d46a5f1d9f8b76961c"
+ "VignetteBuilder": "knitr, rmarkdown",
+ "RoxygenNote": "7.1.2",
+ "NeedsCompilation": "yes",
+ "Author": "Yixuan Qiu [aut, cre], Jiali Mei [aut] (Function interface of matrix operation), Gael Guennebaud [ctb] (Eigenvalue solvers from the 'Eigen' library), Jitse Niesen [ctb] (Eigenvalue solvers from the 'Eigen' library)",
+ "Maintainer": "Yixuan Qiu ",
+ "Repository": "CRAN",
+ "Encoding": "UTF-8"
},
"Rcpp": {
"Package": "Rcpp",
- "Version": "1.0.12",
+ "Version": "1.1.1",
"Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
+ "Title": "Seamless R and C++ Integration",
+ "Date": "2026-01-07",
+ "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Romain\", \"Francois\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"JJ\", \"Allaire\", role = \"aut\", comment = c(ORCID = \"0000-0003-0174-9868\")), person(\"Kevin\", \"Ushey\", role = \"aut\", comment = c(ORCID = \"0000-0003-2880-7407\")), person(\"Qiang\", \"Kou\", role = \"aut\", comment = c(ORCID = \"0000-0001-6786-5453\")), person(\"Nathan\", \"Russell\", role = \"aut\"), person(\"Iñaki\", \"Ucar\", role = \"aut\", comment = c(ORCID = \"0000-0001-6403-5550\")), person(\"Doug\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"John\", \"Chambers\", role = \"aut\"))",
+ "Description": "The 'Rcpp' package provides R functions as well as C++ classes which offer a seamless integration of R and C++. Many R data types and objects can be mapped back and forth to C++ equivalents which facilitates both writing of new code as well as easier integration of third-party libraries. Documentation about 'Rcpp' is provided by several vignettes included in this package, via the 'Rcpp Gallery' site at , the paper by Eddelbuettel and Francois (2011, ), the book by Eddelbuettel (2013, ) and the paper by Eddelbuettel and Balamuta (2018, ); see 'citation(\"Rcpp\")' for details.",
+ "Depends": [
+ "R (>= 3.5.0)"
+ ],
+ "Imports": [
"methods",
"utils"
],
- "Hash": "5ea2700d21e038ace58269ecdbeb9ec0"
+ "Suggests": [
+ "tinytest",
+ "inline",
+ "rbenchmark",
+ "pkgKitten (>= 0.1.2)"
+ ],
+ "URL": "https://www.rcpp.org, https://dirk.eddelbuettel.com/code/rcpp.html, https://github.com/RcppCore/Rcpp",
+ "License": "GPL (>= 2)",
+ "BugReports": "https://github.com/RcppCore/Rcpp/issues",
+ "MailingList": "rcpp-devel@lists.r-forge.r-project.org",
+ "RoxygenNote": "6.1.1",
+ "Encoding": "UTF-8",
+ "VignetteBuilder": "Rcpp",
+ "NeedsCompilation": "yes",
+ "Author": "Dirk Eddelbuettel [aut, cre] (ORCID: ), Romain Francois [aut] (ORCID: ), JJ Allaire [aut] (ORCID: ), Kevin Ushey [aut] (ORCID: ), Qiang Kou [aut] (ORCID: ), Nathan Russell [aut], Iñaki Ucar [aut] (ORCID: ), Doug Bates [aut] (ORCID: ), John Chambers [aut]",
+ "Maintainer": "Dirk Eddelbuettel ",
+ "Repository": "CRAN"
},
"RcppAnnoy": {
"Package": "RcppAnnoy",
- "Version": "0.0.22",
+ "Version": "0.0.23",
"Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "R",
- "Rcpp",
- "methods"
+ "Type": "Package",
+ "Title": "'Rcpp' Bindings for 'Annoy', a Library for Approximate Nearest Neighbors",
+ "Date": "2026-01-12",
+ "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Erik\", \"Bernhardsson\", role = c(\"aut\"), comment = \"Principal author of Annoy\"))",
+ "Description": "'Annoy' is a small C++ library for Approximate Nearest Neighbors written for efficient memory usage as well an ability to load from / save to disk. This package provides an R interface by relying on the 'Rcpp' package, exposing the same interface as the original Python wrapper to 'Annoy'. See for more on 'Annoy'. 'Annoy' is released under Version 2.0 of the Apache License. Also included is a small Windows port of 'mmap' which is released under the MIT license.",
+ "License": "GPL (>= 2)",
+ "Depends": [
+ "R (>= 3.1)"
+ ],
+ "Imports": [
+ "methods",
+ "Rcpp"
+ ],
+ "LinkingTo": [
+ "Rcpp"
+ ],
+ "Suggests": [
+ "tinytest"
],
- "Hash": "f6baa1e06fb6c3724f601a764266cb0d"
+ "URL": "https://github.com/eddelbuettel/rcppannoy, https://dirk.eddelbuettel.com/code/rcpp.annoy.html",
+ "BugReports": "https://github.com/eddelbuettel/rcppannoy/issues",
+ "NeedsCompilation": "yes",
+ "RoxygenNote": "7.3.2",
+ "Encoding": "UTF-8",
+ "VignetteBuilder": "Rcpp",
+ "Author": "Dirk Eddelbuettel [aut, cre] (ORCID: ), Erik Bernhardsson [aut] (Principal author of Annoy)",
+ "Maintainer": "Dirk Eddelbuettel ",
+ "Repository": "CRAN"
},
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- "Version": "0.12.8.2.1",
- "Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "R",
- "Rcpp",
- "methods",
+ "Version": "15.2.3-1",
+ "Source": "Repository",
+ "Type": "Package",
+ "Title": "'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library",
+ "Date": "2025-12-16",
+ "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Romain\", \"Francois\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Doug\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"Binxiang\", \"Ni\", role = \"aut\"), person(\"Conrad\", \"Sanderson\", role = \"aut\", comment = c(ORCID = \"0000-0002-0049-4501\")))",
+ "Description": "'Armadillo' is a templated C++ linear algebra library aiming towards a good balance between speed and ease of use. It provides high-level syntax and functionality deliberately similar to Matlab. It is useful for algorithm development directly in C++, or quick conversion of research code into production environments. It provides efficient classes for vectors, matrices and cubes where dense and sparse matrices are supported. Integer, floating point and complex numbers are supported. A sophisticated expression evaluator (based on template meta-programming) automatically combines several operations to increase speed and efficiency. Dynamic evaluation automatically chooses optimal code paths based on detected matrix structures. Matrix decompositions are provided through integration with LAPACK, or one of its high performance drop-in replacements (such as 'MKL' or 'OpenBLAS'). It can automatically use 'OpenMP' multi-threading (parallelisation) to speed up computationally expensive operations. . The 'RcppArmadillo' package includes the header files from the 'Armadillo' library; users do not need to install 'Armadillo' itself in order to use 'RcppArmadillo'. Starting from release 15.0.0, the minimum compilation standard is C++14 so 'Armadillo' version 14.6.3 is included as a fallback when an R package forces the C++11 standard. Package authors should set a '#define' to select the 'current' version, or select the 'legacy' version (also chosen as default) if they must. See 'GitHub issue #475' for details. . Since release 7.800.0, 'Armadillo' is licensed under Apache License 2; previous releases were under licensed as MPL 2.0 from version 3.800.0 onwards and LGPL-3 prior to that; 'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.",
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+ "Authors@R": "c(person(\"Emmanuel\", \"Paradis\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Emmanuel.Paradis@ird.fr\", comment = c(ORCID = \"0000-0003-3092-2199\")), person(\"Simon\", \"Blomberg\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0003-1062-0839\")), person(\"Ben\", \"Bolker\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0002-2127-0443\")), person(\"Joseph\", \"Brown\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0002-3835-8062\")), person(\"Santiago\", \"Claramunt\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0002-8926-5974\")), person(\"Julien\", \"Claude\", role = c(\"aut\", \"cph\"), , comment = c(ORCID = \"0000-0002-9267-1228\")), person(\"Hoa Sien\", \"Cuong\", role = c(\"aut\", \"cph\")), person(\"Richard\", \"Desper\", role = c(\"aut\", \"cph\")), person(\"Gilles\", \"Didier\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0003-0596-9112\")), person(\"Benoit\", \"Durand\", role = c(\"aut\", \"cph\")), person(\"Julien\", \"Dutheil\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0001-7753-4121\")), person(\"RJ\", \"Ewing\", role = c(\"aut\", \"cph\")), person(\"Olivier\", \"Gascuel\", role = c(\"aut\", \"cph\")), person(\"Thomas\", \"Guillerme\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0003-4325-1275\")), person(\"Christoph\", \"Heibl\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0002-7655-3299\")), person(\"Anthony\", \"Ives\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0001-9375-9523\")), person(\"Bradley\", \"Jones\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0003-4498-1069\")), person(\"Franz\", \"Krah\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0001-7866-7508\")), person(\"Daniel\", \"Lawson\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0002-5311-6213\")), person(\"Vincent\", \"Lefort\", role = c(\"aut\", \"cph\")), person(\"Pierre\", \"Legendre\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0002-3838-3305\")), person(\"Jim\", \"Lemon\", role = c(\"aut\", \"cph\")), person(\"Guillaume\", \"Louvel\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0002-7745-0785\")), person(\"Federico\", \"Marotta\", role = c(\"aut\", \"cph\")), person(\"Eric\", \"Marcon\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0002-5249-321X\")), person(\"Rosemary\", \"McCloskey\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0002-9772-8553\")), person(\"Johan\", \"Nylander\", role = c(\"aut\", \"cph\")), person(\"Rainer\", \"Opgen-Rhein\", role = c(\"aut\", \"cph\")), person(\"Andrei-Alin\", \"Popescu\", role = c(\"aut\", \"cph\")), person(\"Manuela\", \"Royer-Carenzi\", role = c(\"aut\", \"cph\")), person(\"Klaus\", \"Schliep\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0003-2941-0161\")), person(\"Korbinian\", \"Strimmer\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0001-7917-2056\")), person(\"Damien\", \"de Vienne\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0001-9532-5251\")))",
+ "Depends": [
+ "R (>= 3.2.0)"
+ ],
+ "Suggests": [
+ "gee",
+ "expm",
+ "igraph",
+ "phangorn",
+ "xml2"
+ ],
+ "Imports": [
+ "nlme",
"lattice",
+ "graphics",
"methods",
- "nlme",
- "parallel",
"stats",
- "utils"
+ "utils",
+ "parallel",
+ "Rcpp (>= 0.12.0)",
+ "digest"
+ ],
+ "LinkingTo": [
+ "Rcpp"
],
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+ "ZipData": "no",
+ "Description": "Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.",
+ "License": "GPL-2 | GPL-3",
+ "URL": "https://github.com/emmanuelparadis/ape",
+ "BugReports": "https://github.com/emmanuelparadis/ape/issues",
+ "Encoding": "UTF-8",
+ "NeedsCompilation": "yes",
+ "Author": "Emmanuel Paradis [aut, cre, cph] (), Simon Blomberg [aut, cph] (), Ben Bolker [aut, cph] (), Joseph Brown [aut, cph] (), Santiago Claramunt [aut, cph] (), Julien Claude [aut, cph] (), Hoa Sien Cuong [aut, cph], Richard Desper [aut, cph], Gilles Didier [aut, cph] (), Benoit Durand [aut, cph], Julien Dutheil [aut, cph] (), RJ Ewing [aut, cph], Olivier Gascuel [aut, cph], Thomas Guillerme [aut, cph] (), Christoph Heibl [aut, cph] (), Anthony Ives [aut, cph] (), Bradley Jones [aut, cph] (), Franz Krah [aut, cph] (), Daniel Lawson [aut, cph] (), Vincent Lefort [aut, cph], Pierre Legendre [aut, cph] (), Jim Lemon [aut, cph], Guillaume Louvel [aut, cph] (), Federico Marotta [aut, cph], Eric Marcon [aut, cph] (), Rosemary McCloskey [aut, cph] (), Johan Nylander [aut, cph], Rainer Opgen-Rhein [aut, cph], Andrei-Alin Popescu [aut, cph], Manuela Royer-Carenzi [aut, cph], Klaus Schliep [aut, cph] (), Korbinian Strimmer [aut, cph] (), Damien de Vienne [aut, cph] ()",
+ "Maintainer": "Emmanuel Paradis ",
+ "Repository": "CRAN"
},
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"Package": "apeglm",
- "Version": "1.26.0",
+ "Version": "1.32.0",
"Source": "Bioconductor",
- "Repository": "Bioconductor 3.19",
- "Requirements": [
- "GenomicRanges",
- "Rcpp",
- "RcppEigen",
- "RcppNumerical",
- "SummarizedExperiment",
+ "Title": "Approximate posterior estimation for GLM coefficients",
+ "Authors@R": "c( person(\"Anqi\", \"Zhu\", email = \"anqizhu@live.unc.edu\", role = c(\"aut\",\"cre\")), person(\"Joshua\", \"Zitovsky\", role = \"ctb\"), person(\"Joseph\", \"Ibrahim\", role = \"aut\"), person(\"Michael\", \"Love\", role = \"aut\"))",
+ "Maintainer": "Anqi Zhu ",
+ "Description": "apeglm provides Bayesian shrinkage estimators for effect sizes for a variety of GLM models, using approximation of the posterior for individual coefficients.",
+ "VignetteBuilder": "knitr, rmarkdown",
+ "Imports": [
"emdbook",
+ "SummarizedExperiment",
+ "GenomicRanges",
"methods",
"stats",
- "utils"
+ "utils",
+ "Rcpp"
+ ],
+ "Suggests": [
+ "DESeq2",
+ "airway",
+ "knitr",
+ "rmarkdown",
+ "testthat"
],
- "Hash": "db0445903cb0274f9b99abc410768df1"
+ "LinkingTo": [
+ "Rcpp",
+ "RcppEigen",
+ "RcppNumerical"
+ ],
+ "License": "GPL-2",
+ "Encoding": "UTF-8",
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+ "git_url": "https://git.bioconductor.org/packages/apeglm",
+ "git_branch": "RELEASE_3_22",
+ "git_last_commit": "8940580",
+ "git_last_commit_date": "2025-10-29",
+ "Repository": "Bioconductor 3.22",
+ "NeedsCompilation": "yes",
+ "Author": "Anqi Zhu [aut, cre], Joshua Zitovsky [ctb], Joseph Ibrahim [aut], Michael Love [aut]"
},
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"Package": "aplot",
- "Version": "0.2.2",
+ "Version": "0.2.9",
"Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "R",
- "ggfun",
+ "Title": "Decorate a 'ggplot' with Associated Information",
+ "Authors@R": "c( person(given = \"Guangchuang\", family = \"Yu\", email = \"guangchuangyu@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6485-8781\")), person(\"Shuangbin\", \"Xu\", email = \"xshuangbin@163.com\", role = \"ctb\", comment = c(ORCID=\"0000-0003-3513-5362\")), person(given = \"Thomas\", family = \"Hackl\", email = \"thackl@mit.edu\", role = \"ctb\") )",
+ "Description": "For many times, we are not just aligning plots as what 'cowplot' and 'patchwork' did. Users would like to align associated information that requires axes to be exactly matched in subplots, e.g. hierarchical clustering with a heatmap. Inspired by the 'Method 2' in 'ggtree' (G Yu (2018) ), 'aplot' provides utilities to aligns associated subplots to a main plot at different sides (left, right, top and bottom) with axes exactly matched.",
+ "Depends": [
+ "R (>= 4.1.0)"
+ ],
+ "Imports": [
+ "ggfun (>= 0.1.3)",
"ggplot2",
"ggplotify",
+ "patchwork",
"magrittr",
"methods",
- "patchwork",
- "utils"
+ "utils",
+ "yulab.utils (>= 0.1.9)",
+ "pillar"
],
- "Hash": "869a35e6d38fe9936eb578e09091842b"
+ "Suggests": [
+ "ggtree"
+ ],
+ "URL": "https://github.com/YuLab-SMU/aplot, https://yulab-smu.top/aplot/",
+ "License": "Artistic-2.0",
+ "Encoding": "UTF-8",
+ "RoxygenNote": "7.3.2",
+ "NeedsCompilation": "no",
+ "Author": "Guangchuang Yu [aut, cre] (ORCID: ), Shuangbin Xu [ctb] (ORCID: ), Thomas Hackl [ctb]",
+ "Maintainer": "Guangchuang Yu ",
+ "Repository": "CRAN"
},
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"Package": "ashr",
"Version": "2.2-63",
"Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
+ "Encoding": "UTF-8",
+ "Type": "Package",
+ "Maintainer": "Peter Carbonetto ",
+ "Authors@R": "c(person(\"Matthew\",\"Stephens\",role=\"aut\", email=\"mstephens@uchicago.edu\"), person(\"Peter\",\"Carbonetto\",role=c(\"aut\",\"cre\"), email=\"pcarbo@uchicago.edu\"), person(\"Chaoxing\",\"Dai\",role=\"ctb\"), person(\"David\",\"Gerard\",role=\"aut\"), person(\"Mengyin\",\"Lu\",role=\"aut\"), person(\"Lei\",\"Sun\",role=\"aut\"), person(\"Jason\",\"Willwerscheid\",role=\"aut\"), person(\"Nan\",\"Xiao\",role=\"aut\"), person(\"Mazon\",\"Zeng\",role=\"ctb\"))",
+ "Date": "2023-08-21",
+ "Title": "Methods for Adaptive Shrinkage, using Empirical Bayes",
+ "Description": "The R package 'ashr' implements an Empirical Bayes approach for large-scale hypothesis testing and false discovery rate (FDR) estimation based on the methods proposed in M. Stephens, 2016, \"False discovery rates: a new deal\", . These methods can be applied whenever two sets of summary statistics---estimated effects and standard errors---are available, just as 'qvalue' can be applied to previously computed p-values. Two main interfaces are provided: ash(), which is more user-friendly; and ash.workhorse(), which has more options and is geared toward advanced users. The ash() and ash.workhorse() also provides a flexible modeling interface that can accommodate a variety of likelihoods (e.g., normal, Poisson) and mixture priors (e.g., uniform, normal).",
+ "Depends": [
+ "R (>= 3.1.0)"
+ ],
+ "Imports": [
"Matrix",
- "R",
- "Rcpp",
- "SQUAREM",
- "etrunct",
+ "stats",
"graphics",
- "invgamma",
+ "Rcpp (>= 0.10.5)",
+ "truncnorm",
"mixsqp",
- "stats",
- "truncnorm"
+ "SQUAREM",
+ "etrunct",
+ "invgamma"
+ ],
+ "Suggests": [
+ "testthat",
+ "knitr",
+ "rmarkdown",
+ "ggplot2",
+ "REBayes"
+ ],
+ "LinkingTo": [
+ "Rcpp"
],
- "Hash": "d5b252e570ccffbc8fec77827c585635"
+ "License": "GPL (>= 3)",
+ "NeedsCompilation": "yes",
+ "URL": "https://github.com/stephens999/ashr",
+ "BugReports": "https://github.com/stephens999/ashr/issues",
+ "VignetteBuilder": "knitr",
+ "RoxygenNote": "7.1.2",
+ "Author": "Matthew Stephens [aut], Peter Carbonetto [aut, cre], Chaoxing Dai [ctb], David Gerard [aut], Mengyin Lu [aut], Lei Sun [aut], Jason Willwerscheid [aut], Nan Xiao [aut], Mazon Zeng [ctb]",
+ "Repository": "CRAN"
},
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"Package": "askpass",
- "Version": "1.2.0",
+ "Version": "1.2.1",
"Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "sys"
+ "Type": "Package",
+ "Title": "Password Entry Utilities for R, Git, and SSH",
+ "Authors@R": "person(\"Jeroen\", \"Ooms\", role = c(\"aut\", \"cre\"), email = \"jeroenooms@gmail.com\", comment = c(ORCID = \"0000-0002-4035-0289\"))",
+ "Description": "Cross-platform utilities for prompting the user for credentials or a passphrase, for example to authenticate with a server or read a protected key. Includes native programs for MacOS and Windows, hence no 'tcltk' is required. Password entry can be invoked in two different ways: directly from R via the askpass() function, or indirectly as password-entry back-end for 'ssh-agent' or 'git-credential' via the SSH_ASKPASS and GIT_ASKPASS environment variables. Thereby the user can be prompted for credentials or a passphrase if needed when R calls out to git or ssh.",
+ "License": "MIT + file LICENSE",
+ "URL": "https://r-lib.r-universe.dev/askpass",
+ "BugReports": "https://github.com/r-lib/askpass/issues",
+ "Encoding": "UTF-8",
+ "Imports": [
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+ ],
+ "RoxygenNote": "7.2.3",
+ "Suggests": [
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+ ],
+ "Language": "en-US",
+ "NeedsCompilation": "yes",
+ "Author": "Jeroen Ooms [aut, cre] ()",
+ "Maintainer": "Jeroen Ooms ",
+ "Repository": "CRAN"
+ },
+ "assertthat": {
+ "Package": "assertthat",
+ "Version": "0.2.1",
+ "Source": "Repository",
+ "Title": "Easy Pre and Post Assertions",
+ "Authors@R": "person(\"Hadley\", \"Wickham\", , \"hadley@rstudio.com\", c(\"aut\", \"cre\"))",
+ "Description": "An extension to stopifnot() that makes it easy to declare the pre and post conditions that you code should satisfy, while also producing friendly error messages so that your users know what's gone wrong.",
+ "License": "GPL-3",
+ "Imports": [
+ "tools"
+ ],
+ "Suggests": [
+ "testthat",
+ "covr"
],
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+ "NeedsCompilation": "no",
+ "Author": "Hadley Wickham [aut, cre]",
+ "Maintainer": "Hadley Wickham ",
+ "Repository": "CRAN",
+ "Encoding": "UTF-8"
+ },
+ "assorthead": {
+ "Package": "assorthead",
+ "Version": "1.4.0",
+ "Source": "Bioconductor",
+ "Date": "2025-10-27",
+ "Title": "Assorted Header-Only C++ Libraries",
+ "Authors@R": "person(\"Aaron\", \"Lun\", role=c(\"cre\", \"aut\"), email=\"infinite.monkeys.with.keyboards@gmail.com\")",
+ "Description": "Vendors an assortment of useful header-only C++ libraries. Bioconductor packages can use these libraries in their own C++ code by LinkingTo this package without introducing any additional dependencies. The use of a central repository avoids duplicate vendoring of libraries across multiple R packages, and enables better coordination of version updates across cohorts of interdependent C++ libraries.",
+ "License": "MIT + file LICENSE",
+ "Suggests": [
+ "knitr",
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+ "BiocStyle"
+ ],
+ "VignetteBuilder": "knitr",
+ "URL": "https://github.com/LTLA/assorthead",
+ "BugReports": "https://github.com/LTLA/assorthead/issues",
+ "Encoding": "UTF-8",
+ "biocViews": "SingleCell, QualityControl, Normalization, DataRepresentation, DataImport, DifferentialExpression, Alignment",
+ "git_url": "https://git.bioconductor.org/packages/assorthead",
+ "git_branch": "RELEASE_3_22",
+ "git_last_commit": "9255f2f",
+ "git_last_commit_date": "2025-10-29",
+ "Repository": "Bioconductor 3.22",
+ "NeedsCompilation": "no",
+ "Author": "Aaron Lun [cre, aut]",
+ "Maintainer": "Aaron Lun "
},
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"Package": "babelgene",
"Version": "22.9",
"Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "R",
+ "Type": "Package",
+ "Title": "Gene Orthologs for Model Organisms in a Tidy Data Format",
+ "Authors@R": "person(\"Igor\", \"Dolgalev\", , \"igor.dolgalev@nyumc.org\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4451-126X\"))",
+ "Description": "Genomic analysis of model organisms frequently requires the use of databases based on human data or making comparisons to patient-derived resources. This requires harmonization of gene names into the same gene space. The 'babelgene' R package converts between human and non-human gene orthologs/homologs. The package integrates orthology assertion predictions sourced from multiple databases as compiled by the HGNC Comparison of Orthology Predictions (HCOP) (Wright et al. 2005 , Eyre et al. 2007 , Seal et al. 2011 ).",
+ "License": "MIT + file LICENSE",
+ "URL": "https://igordot.github.io/babelgene/",
+ "BugReports": "https://github.com/igordot/babelgene/issues",
+ "Depends": [
+ "R (>= 3.4)"
+ ],
+ "Imports": [
"dplyr",
"methods",
"rlang"
],
- "Hash": "8288e81d0c2c3272603f6ef394ffa6fd"
+ "Suggests": [
+ "covr",
+ "knitr",
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+ "testthat (>= 3.0.0)"
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+ "Encoding": "UTF-8",
+ "RoxygenNote": "7.2.1",
+ "NeedsCompilation": "no",
+ "Author": "Igor Dolgalev [aut, cre] ()",
+ "Maintainer": "Igor Dolgalev ",
+ "Repository": "CRAN"
},
"backports": {
"Package": "backports",
- "Version": "1.4.1",
+ "Version": "1.5.0",
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- "Repository": "CRAN",
- "Requirements": [
- "R"
- ],
- "Hash": "c39fbec8a30d23e721980b8afb31984c"
+ "Type": "Package",
+ "Title": "Reimplementations of Functions Introduced Since R-3.0.0",
+ "Authors@R": "c( person(\"Michel\", \"Lang\", NULL, \"michellang@gmail.com\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0001-9754-0393\")), person(\"Duncan\", \"Murdoch\", NULL, \"murdoch.duncan@gmail.com\", role = c(\"aut\")), person(\"R Core Team\", role = \"aut\"))",
+ "Maintainer": "Michel Lang ",
+ "Description": "Functions introduced or changed since R v3.0.0 are re-implemented in this package. The backports are conditionally exported in order to let R resolve the function name to either the implemented backport, or the respective base version, if available. Package developers can make use of new functions or arguments by selectively importing specific backports to support older installations.",
+ "URL": "https://github.com/r-lib/backports",
+ "BugReports": "https://github.com/r-lib/backports/issues",
+ "License": "GPL-2 | GPL-3",
+ "NeedsCompilation": "yes",
+ "ByteCompile": "yes",
+ "Depends": [
+ "R (>= 3.0.0)"
+ ],
+ "Encoding": "UTF-8",
+ "RoxygenNote": "7.3.1",
+ "Author": "Michel Lang [cre, aut] (), Duncan Murdoch [aut], R Core Team [aut]",
+ "Repository": "CRAN"
},
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"Package": "base64enc",
- "Version": "0.1-3",
+ "Version": "0.1-6",
"Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "R"
+ "Title": "Tools for 'base64' Encoding",
+ "Author": "Simon Urbanek [aut, cre, cph] (https://urbanek.nz, ORCID: )",
+ "Authors@R": "person(\"Simon\", \"Urbanek\", role=c(\"aut\",\"cre\",\"cph\"), email=\"Simon.Urbanek@r-project.org\", comment=c(\"https://urbanek.nz\", ORCID=\"0000-0003-2297-1732\"))",
+ "Maintainer": "Simon Urbanek ",
+ "Depends": [
+ "R (>= 2.9.0)"
+ ],
+ "Enhances": [
+ "png"
],
- "Hash": "543776ae6848fde2f48ff3816d0628bc"
+ "Description": "Tools for handling 'base64' encoding. It is more flexible than the orphaned 'base64' package.",
+ "License": "GPL-2 | GPL-3",
+ "URL": "https://www.rforge.net/base64enc",
+ "BugReports": "https://github.com/s-u/base64enc/issues",
+ "NeedsCompilation": "yes",
+ "Repository": "CRAN",
+ "Encoding": "UTF-8"
},
"batchelor": {
"Package": "batchelor",
- "Version": "1.20.0",
+ "Version": "1.26.0",
"Source": "Bioconductor",
- "Repository": "Bioconductor 3.19",
- "Requirements": [
+ "Date": "2025-03-13",
+ "Title": "Single-Cell Batch Correction Methods",
+ "Authors@R": "c(person(\"Aaron\", \"Lun\", role = c(\"aut\", \"cre\"), email = \"infinite.monkeys.with.keyboards@gmail.com\"), person(\"Laleh\", \"Haghverdi\", role=\"ctb\"))",
+ "Depends": [
+ "SingleCellExperiment"
+ ],
+ "Imports": [
+ "SummarizedExperiment",
+ "S4Vectors",
"BiocGenerics",
+ "Rcpp",
+ "stats",
+ "methods",
+ "utils",
+ "igraph",
"BiocNeighbors",
- "BiocParallel",
"BiocSingular",
- "DelayedArray",
- "DelayedMatrixStats",
"Matrix",
- "Rcpp",
+ "SparseArray",
+ "DelayedArray (>= 0.31.5)",
+ "DelayedMatrixStats",
+ "BiocParallel",
+ "scuttle",
"ResidualMatrix",
- "S4Vectors",
"ScaledMatrix",
- "SingleCellExperiment",
- "SummarizedExperiment",
- "beachmat",
- "igraph",
- "methods",
- "scuttle",
- "stats",
- "utils"
+ "beachmat"
+ ],
+ "Suggests": [
+ "testthat",
+ "BiocStyle",
+ "knitr",
+ "rmarkdown",
+ "scran",
+ "scater",
+ "bluster",
+ "scRNAseq"
+ ],
+ "biocViews": "Sequencing, RNASeq, Software, GeneExpression, Transcriptomics, SingleCell, BatchEffect, Normalization",
+ "LinkingTo": [
+ "Rcpp"
],
- "Hash": "ec5dcf85cdf644b078d02deaf27a3bfd"
+ "Description": "Implements a variety of methods for batch correction of single-cell (RNA sequencing) data. This includes methods based on detecting mutually nearest neighbors, as well as several efficient variants of linear regression of the log-expression values. Functions are also provided to perform global rescaling to remove differences in depth between batches, and to perform a principal components analysis that is robust to differences in the numbers of cells across batches.",
+ "License": "GPL-3",
+ "NeedsCompilation": "yes",
+ "VignetteBuilder": "knitr",
+ "SystemRequirements": "C++11",
+ "RoxygenNote": "7.3.2",
+ "git_url": "https://git.bioconductor.org/packages/batchelor",
+ "git_branch": "RELEASE_3_22",
+ "git_last_commit": "8a9df0d",
+ "git_last_commit_date": "2025-10-29",
+ "Repository": "Bioconductor 3.22",
+ "Author": "Aaron Lun [aut, cre], Laleh Haghverdi [ctb]",
+ "Maintainer": "Aaron Lun "
},
"bbmle": {
"Package": "bbmle",
"Version": "1.0.25.1",
"Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "MASS",
- "Matrix",
- "R",
- "bdsmatrix",
+ "Title": "Tools for General Maximum Likelihood Estimation",
+ "Description": "Methods and functions for fitting maximum likelihood models in R. This package modifies and extends the 'mle' classes in the 'stats4' package.",
+ "Authors@R": "c(person(\"Ben\",\"Bolker\",email=\"bolker@mcmaster.ca\",role=c(\"aut\",\"cre\"), comment=c(ORCID=\"0000-0002-2127-0443\")), person(\"R Development Core Team\",role=c(\"aut\")), person(\"Iago Giné-Vázquez\", role=c(\"ctb\")) )",
+ "Depends": [
+ "R (>= 3.0.0)",
+ "stats4"
+ ],
+ "Imports": [
+ "stats",
+ "numDeriv",
"lattice",
+ "MASS",
"methods",
- "mvtnorm",
- "numDeriv",
- "stats",
- "stats4"
+ "bdsmatrix",
+ "Matrix",
+ "mvtnorm"
],
- "Hash": "f32b6a1dfc5c80504326aa3474b10fe6"
+ "Suggests": [
+ "emdbook",
+ "rms",
+ "ggplot2",
+ "RUnit",
+ "MuMIn",
+ "AICcmodavg",
+ "Hmisc",
+ "optimx (>= 2013.8.6)",
+ "knitr",
+ "testthat"
+ ],
+ "VignetteBuilder": "knitr",
+ "BuildVignettes": "yes",
+ "License": "GPL",
+ "URL": "https://github.com/bbolker/bbmle",
+ "Collate": "'mle2-class.R' 'mle2-methods.R' 'mle.R' 'confint.R' 'predict.R' 'profile.R' 'update.R' 'dists.R' 'IC.R' 'slice.R' 'impsamp.R' 'TMB.R'",
+ "RoxygenNote": "7.1.0",
+ "Encoding": "UTF-8",
+ "NeedsCompilation": "no",
+ "Author": "Ben Bolker [aut, cre] (