Workflow separations & Correlation Analysis by sktpndt97 · Pull Request #48 · wejlab/animalcules

sktpndt97 · 2021-07-12T02:50:49Z

Workflow Separation

Created three different workflows: Microbial, Host Expression, and Integrative Analysis.
Microbial is the same as 'animalcules' before any changes, and Integrative Analysis includes the Correlations tab. Host Expression still needs some more functionality to be filled out
Workflows will only pop up if the corresponding assay is present

Correlation Analysis

Users can select two assays to correlate against one another. Subsequently, can do Co-Occurence Network and Enrichment analyses

Also updated vignettes to include instructions for usage.

…o longer relying on shiny app to do so

…top 10 summary table

…done on shiny. Also, integrated enrichment with hypeR

…lations would show up

…e + co-occurence network)

…ng anything with it

…, Correlates)

…ment tables

…iAssayExperiment. Also, fixed a problem where new ssGSEA scores would not insert

…Workflows

…s and enrichment

…e assays

Saket Pandit added 30 commits March 27, 2021 19:42

Correlation shiny UI

6e728db

Correlations shiny server

85c3535

Correlations R functions

0058cec

Adding 'updateAssays' session function to keep track of assays in MAE

cbd17b5

Man files for these functions

f0a4fd1

Man file for rd_MAE

80d70a4

slight change to corr_func, changed name

de1b1ff

updated to also include correlations

a74b625

Added mae.assays

06d6edd

Updated to include Workflow tabs + Correlations

de27a01

Fixed a typo

55d6506

Fixed another typo

ddb2e94

manual for genes_gsva_dimred.R function

59a81b1

Function for GSVA analysis / dimension reduction

e377c9d

Including genes_dimred_gsva

34bbb20

Adding in a GSVA tab

1bba342

Server function for GSVA tab

14b069f

UI function for GSVA tab

da8d479

Adding in MSigDB collections, used in GSVA tab

814a487

Now includes genes_dimred_gsva.R

9b700c6

Commented out tags$style(appCSS)

e43ff71

Modified so that the function now creates the plot + summary table. N…

a4cc179

…o longer relying on shiny app to do so

Fixed some small typos, made calc_sig *slightly* faster

58f74bb

Modified corr_func so that it will also produce a plot, summary, and …

b519c41

…top 10 summary table

Modified shiny scripts so that none of the "correlations" section is …

4d71c06

…done on shiny. Also, integrated enrichment with hypeR

added hypeR library

ac5e8aa

Changed so that enrichment is also not done on Rshiny

c8c674c

No longer need to connect to enrichR, using hypeR

45f47d3

Including updated corr_func and enrich_cors

cf27095

Now includes summary_cors, heatmap_cors, and enrich_cors

8e17f7a

Saket Pandit added 30 commits June 23, 2021 20:57

Fixed so that it will work even if Group_Size = 1

87baf50

Fixed issue where not all groups were displaying, only positive corre…

d230331

…lations would show up

Added in interactive summary table for the split conditions (main pag…

2bbd8b6

…e + co-occurence network)

Forgot to add "@export" for the function

bd70ee6

Added "@export", and also sort the rows_selected parameter before doi…

cfb1443

…ng anything with it

Changed to match the new column names produced by summary_cors (Group…

42a90b6

…, Correlates)

Added interactive enrichment table

dce8d80

Better documentation

306aff6

Added descriptive text for clearer instructions

d3945ff

commented out loading R library (testing)

37081ab

Commented out GO_Biological_Process (temp)

3447fc4

Added more descriptive text, specifically for split conditions

a3bda8b

Only allowing single row selection for co-occurence networks + enrich…

6bf7aa4

…ment tables

Created a separate function to insert the ssGSEA scores into the Mult…

e6f7ed6

…iAssayExperiment. Also, fixed a problem where new ssGSEA scores would not insert

Fixed example

a7caa5d

Changed gene names from Ensembl ID to Gene Symbol

e6b6fea

Integrates use of insert_into_MAE() and path_proj()

09ee2dd

Cleaned up code (clearer commenting/documentation)

2402a45

Fixed issue with reading in assays and displaying the correct Tabs / …

45b0dd7

…Workflows

Cleaned up code, comments and documentation

9782eb5

Includes insert_into_MAE()

9ba37ac

Small changes to be compliant with Bioconductor checks

0c080a7

Aesthetic changes to the example

ae85bd1

Updated to include instructions and examples for co-occurence network…

df32a6c

…s and enrichment

Fixed issue with deprecation

8f22030

Got rid of the devtools() line, ready for final pull request

9c944fc

Removed a browser() command used during debugging

05eb01a

Removed another browser() command

a27c7ec

Fixed a problem with corr_func, is now able to handle NA values in th…

fc3bb1d

…e assays

Fixed issue where gsva data did not insert into MAE

fe1cfa3

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Workflow separations & Correlation Analysis#48

Workflow separations & Correlation Analysis#48
sktpndt97 wants to merge 111 commits into
wejlab:develfrom
sktpndt97:master

sktpndt97 commented Jul 12, 2021

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

1 participant

Conversation

sktpndt97 commented Jul 12, 2021