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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

    243 77

  2. Pando Pando Public

    Multiome GRN inference.

    R 135 23

  3. scMultiome_analysis_vignette scMultiome_analysis_vignette Public

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

    71 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 40 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 48 repositories
  • pygpcca_speedup_analysis Public

    Experiment with gradient-based optimization for pyGPCCA

    quadbio/pygpcca_speedup_analysis’s past year of commit activity
    Python 0 BSD-3-Clause 0 0 0 Updated Feb 17, 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 448 0 2 Updated Feb 17, 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 Feb 16, 2026
  • scembed Public

    Run embedding comparisons for single-cell data

    quadbio/scembed’s past year of commit activity
    Python 4 MIT 1 0 4 Updated Feb 16, 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 13 MIT 3 4 1 Updated Feb 16, 2026
  • cell-annotator Public

    Automatically annotate cell types, consistently across samples.

    quadbio/cell-annotator’s past year of commit activity
    Python 19 MIT 1 3 2 Updated Feb 16, 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 30 0 0 Updated Feb 15, 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 Feb 9, 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
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