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@quadbio

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

    200 66

  2. Pando Pando Public

    Multiome GRN inference.

    R 123 22

  3. scMultiome_analysis_vignette scMultiome_analysis_vignette Public

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

    57 14

  4. VoxHunt VoxHunt Public

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

    HTML 46 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 34 4

  6. simspec simspec Public

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

    R 31 3

Repositories

Showing 10 of 34 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 4 MIT 0 3 1 Updated May 28, 2025
  • slurm_sweep Public

    Hyperparameter sweeps on SLURM clusters

    quadbio/slurm_sweep’s past year of commit activity
    Python 2 MIT 0 1 1 Updated May 26, 2025
  • morphodynamics_human_brain_organoid Public
    quadbio/morphodynamics_human_brain_organoid’s past year of commit activity
    Jupyter Notebook 1 MIT 1 0 0 Updated May 23, 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 33 0 0 Updated May 15, 2025
  • ecosystem-packages Public Forked from scverse/ecosystem-packages

    Registry for scverse ecosystem packages (https://scverse.org/packages/#ecosystem)

    quadbio/ecosystem-packages’s past year of commit activity
    Python 0 BSD-3-Clause 51 0 0 Updated May 2, 2025
  • iNeuron_morphogens Public
    quadbio/iNeuron_morphogens’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Apr 17, 2025
  • cell-annotator Public

    Automatically annotate cell types, consistently across samples.

    quadbio/cell-annotator’s past year of commit activity
    Python 13 MIT 1 5 1 Updated Apr 17, 2025
  • BVO_fate_and_state_transitions Public
    quadbio/BVO_fate_and_state_transitions’s past year of commit activity
    R 4 GPL-3.0 0 0 0 Updated Apr 11, 2025
  • scib-metrics Public Forked from YosefLab/scib-metrics

    Accelerated, Python-only, single-cell integration benchmarking metrics

    quadbio/scib-metrics’s past year of commit activity
    Python 0 BSD-3-Clause 16 0 0 Updated Apr 10, 2025
  • simple_slurm Public Forked from amq92/simple_slurm

    A simple Python wrapper for Slurm with flexibility in mind.

    quadbio/simple_slurm’s past year of commit activity
    Python 0 AGPL-3.0 25 0 0 Updated Apr 8, 2025
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