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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

    233 75

  2. Pando Pando Public

    Multiome GRN inference.

    R 131 22

  3. scMultiome_analysis_vignette scMultiome_analysis_vignette Public

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

    68 15

  4. VoxHunt VoxHunt Public

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

    HTML 47 6

  5. 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

  6. simspec simspec Public

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

    R 37 3

Repositories

Showing 10 of 44 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 436 0 1 Updated Dec 23, 2025
  • slurm_sweep Public

    Hyperparameter sweeps on SLURM clusters

    quadbio/slurm_sweep’s past year of commit activity
    Python 4 MIT 1 0 2 Updated Dec 22, 2025
  • cell-annotator Public

    Automatically annotate cell types, consistently across samples.

    quadbio/cell-annotator’s past year of commit activity
    Python 17 MIT 1 3 2 Updated Dec 22, 2025
  • scembed Public

    Run embedding comparisons for single-cell data

    quadbio/scembed’s past year of commit activity
    Python 3 MIT 1 0 4 Updated Dec 22, 2025
  • 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 10 MIT 2 4 3 Updated Dec 22, 2025
  • 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
  • pysimspec Public

    Python implementation of simspec (for RSS/CSS)

    quadbio/pysimspec’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Dec 18, 2025
  • organoid_patterning_screen Public

    This repository contains the code to reproduce the analysis in the manuscript "Systematic neural organoid scRNA-seq screens measure morphogen response" (Sanchís-Calleja, Azbukina et al, 2025)

    quadbio/organoid_patterning_screen’s past year of commit activity
    Jupyter Notebook 2 0 0 0 Updated Dec 15, 2025
  • 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 Dec 14, 2025
  • iNeuron_patterning Public
    quadbio/iNeuron_patterning’s past year of commit activity
    Jupyter Notebook 7 1 0 0 Updated Oct 22, 2025
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