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QuaDBio Lab

Quantitative Developmental Biology Lab

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  1. scRNAseq_analysis_vignette scRNAseq_analysis_vignette Public

    Tutorial for scRNA-seq data analysis beginners using R

    241 77

  2. Pando Pando Public

    Multiome GRN inference.

    R 134 22

  3. scMultiome_analysis_vignette scMultiome_analysis_vignette Public

    Tutorial of single-cell RNA-ATAC multiomic sequencing data analysis

    69 15

  4. VoxHunt VoxHunt Public

    VoxHunt: Resolving human brain organoid heterogeneity through single-cell genomic comparison to spatial brain maps

    HTML 47 6

  5. simspec simspec Public

    Calculation of Reference/Cluster Similarity Spectrum (RSS/CSS)

    R 39 3

  6. primate_cerebral_organoids primate_cerebral_organoids Public

    Reusable scripts and functions archive for the paper "Organoid single-cell genomic atlas uncovers human-specific features of brain development" (https://www.nature.com/articles/s41586-019-1654-9)

    R 38 5

Repositories

Showing 10 of 46 repositories
  • scvi-tools-public Public Forked from scverse/scvi-tools

    Deep probabilistic analysis of single-cell and spatial omics data

    quadbio/scvi-tools-public’s past year of commit activity
    Python 0 BSD-3-Clause 443 0 1 Updated Feb 3, 2026
  • cell-annotator Public

    Automatically annotate cell types, consistently across samples.

    quadbio/cell-annotator’s past year of commit activity
    Python 18 MIT 1 3 2 Updated Feb 2, 2026
  • scembed Public

    Run embedding comparisons for single-cell data

    quadbio/scembed’s past year of commit activity
    Python 3 MIT 1 0 4 Updated Feb 2, 2026
  • slurm_sweep Public

    Hyperparameter sweeps on SLURM clusters

    quadbio/slurm_sweep’s past year of commit activity
    Python 4 MIT 1 0 2 Updated Feb 2, 2026
  • cellmapper Public

    k-NN-based mapping of cells across representations to transfer labels, embeddings, and expression values.

    quadbio/cellmapper’s past year of commit activity
    Python 12 MIT 3 4 1 Updated Feb 2, 2026
  • hydra-sweeper-explicit Public

    Sweeper plugin for explicit multirun configs in hydra

    quadbio/hydra-sweeper-explicit’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Jan 30, 2026
  • analysis_template Public template

    Simple template repo for single-cell/spatial analysis

    quadbio/analysis_template’s past year of commit activity
    Jupyter Notebook 0 BSD-3-Clause 0 0 0 Updated Jan 29, 2026
  • transcriptomic_clustering Public Forked from AllenInstitute/transcriptomic_clustering

    Allen Institute Transcriptomic Clustering Pipeline

    quadbio/transcriptomic_clustering’s past year of commit activity
    Python 0 3 0 0 Updated Jan 28, 2026
  • novae Public Forked from MICS-Lab/novae

    Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many other features.

    quadbio/novae’s past year of commit activity
    Python 2 BSD-3-Clause 12 0 0 Updated Jan 15, 2026
  • sopa Public Forked from gustaveroussy/sopa

    Technology-invariant pipeline for spatial omics analysis (Xenium / MERSCOPE / CosMx / PhenoCycler / MACSima / Hyperion) that scales to millions of cells

    quadbio/sopa’s past year of commit activity
    Python 0 BSD-3-Clause 42 0 0 Updated Dec 18, 2025
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