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Raychaudhuri Lab

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  1. harmony harmony Public

    Fast, sensitive and accurate integration of single-cell data with Harmony

    R 568 102

  2. presto presto Public

    Fast Wilcoxon and auROC

    Jupyter Notebook 180 36

  3. symphony symphony Public

    Efficient and precise single-cell reference atlas mapping with Symphony

    Jupyter Notebook 104 22

  4. SCENT SCENT Public

    Single-Cell ENhancer Target gene mapping using multimodal data with ATAC + RNA

    R 74 11

  5. HLA_analyses_tutorial HLA_analyses_tutorial Public

    A thorough tutorial on HLA imputation and association, accompanying our manuscript "Tutorial: A statistical genetics guide to identifying HLA alleles driving complex disease"

    Jupyter Notebook 67 14

  6. LISI LISI Public

    Methods to compute Local Inverse Simpson's Index (LISI)

    R 61 5

Repositories

Showing 10 of 68 repositories
  • cna Public

    Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-cell datasets.

    immunogenomics/cna’s past year of commit activity
    Python 49 GPL-3.0 5 1 0 Updated Apr 29, 2025
  • starCAT Public

    Implements *CellAnnotator (aka *CAT/starCAT), annotating scRNA-Seq with predefined gene expression programs

    immunogenomics/starCAT’s past year of commit activity
    Jupyter Notebook 22 MIT 3 0 1 Updated Apr 29, 2025
  • GeNA-applied Public

    Code and analyses supporting the GeNA single-cell csaQTL manuscript.

    immunogenomics/GeNA-applied’s past year of commit activity
    Jupyter Notebook 2 GPL-3.0 0 0 0 Updated Apr 29, 2025
  • cna-display Public

    Generation of display items for CNA paper

    immunogenomics/cna-display’s past year of commit activity
    Jupyter Notebook 3 MIT 1 0 0 Updated Apr 28, 2025
  • cna-sim Public

    Simulation code for CNA evaluation

    immunogenomics/cna-sim’s past year of commit activity
    Python 0 GPL-3.0 0 1 0 Updated Apr 28, 2025
  • SCENT Public

    Single-Cell ENhancer Target gene mapping using multimodal data with ATAC + RNA

    immunogenomics/SCENT’s past year of commit activity
    R 74 11 1 0 Updated Apr 21, 2025
  • snATAC_benchmark Public

    Code corresponding to Weinand et al., Defining effective strategies to integrate multi-sample single-nucleus ATAC-seq datasets via a multimodal-guided approach, Submitted.

    immunogenomics/snATAC_benchmark’s past year of commit activity
    Jupyter Notebook 1 GPL-3.0 1 0 0 Updated Apr 8, 2025
  • craft-seq Public

    Code for analysis of CRAFT-seq data

    immunogenomics/craft-seq’s past year of commit activity
    Jupyter Notebook 1 0 0 0 Updated Mar 31, 2025
  • TCAT_analysis Public

    Code repository for TCAT analyses

    immunogenomics/TCAT_analysis’s past year of commit activity
    Jupyter Notebook 7 2 0 0 Updated Mar 13, 2025
  • amp_phase1_ra Public

    🌾 Zhang, et al, Nature Immunology, 2019. Use single-cell transcriptomics and proteomics to study autoimmune diseases.

    immunogenomics/amp_phase1_ra’s past year of commit activity
    Jupyter Notebook 20 GPL-3.0 13 1 0 Updated Mar 11, 2025
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