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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

    251 82

  2. Pando Pando Public

    Multiome GRN inference.

    R 135 24

  3. scMultiome_analysis_vignette scMultiome_analysis_vignette Public

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

    78 17

  4. VoxHunt VoxHunt Public

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

    HTML 48 6

  5. simspec simspec Public

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

    R 40 3

  6. RNAseq_tutorial RNAseq_tutorial Public

    40 14

Repositories

Showing 10 of 50 repositories
  • 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 13 MIT 3 4 1 Updated Apr 6, 2026
  • scembed Public

    Run embedding comparisons for single-cell data

    quadbio/scembed’s past year of commit activity
    Python 5 MIT 1 0 4 Updated Apr 6, 2026
  • cell-annotator Public

    Automatically annotate cell types, consistently across samples.

    quadbio/cell-annotator’s past year of commit activity
    Python 20 MIT 2 3 3 Updated Apr 6, 2026
  • slurm_sweep Public

    Hyperparameter sweeps on SLURM clusters

    quadbio/slurm_sweep’s past year of commit activity
    Python 5 MIT 2 1 2 Updated Apr 6, 2026
  • 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 452 0 0 Updated Apr 1, 2026
  • simspec Public

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

    quadbio/simspec’s past year of commit activity
    R 40 3 4 0 Updated Mar 31, 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 Mar 31, 2026
  • squidpy Public Forked from scverse/squidpy

    Spatial Single Cell Analysis in Python

    quadbio/squidpy’s past year of commit activity
    Python 0 BSD-3-Clause 111 0 0 Updated Mar 23, 2026
  • scvi-tutorials Public Forked from scverse/scvi-tutorials

    Notebooks used in scvi-tools tutorials

    quadbio/scvi-tutorials’s past year of commit activity
    Jupyter Notebook 0 BSD-3-Clause 32 0 0 Updated Mar 18, 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 47 0 0 Updated Feb 26, 2026
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