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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 556 103

  2. presto presto Public

    Fast Wilcoxon and auROC

    Jupyter Notebook 175 36

  3. symphony symphony Public

    Efficient and precise single-cell reference atlas mapping with Symphony

    Jupyter Notebook 103 23

  4. SCENT SCENT Public

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

    R 72 10

  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 66 14

  6. LISI LISI Public

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

    R 61 5

Repositories

Showing 10 of 68 repositories
  • 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 19 GPL-3.0 13 1 0 Updated Mar 11, 2025
  • 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 48 GPL-3.0 5 0 0 Updated Feb 28, 2025
  • minecraft-seq Public

    Code for analysis of MINECRAFT-seq data

    immunogenomics/minecraft-seq’s past year of commit activity
    Jupyter Notebook 1 0 0 0 Updated Feb 19, 2025
  • EarlyLate_RNA_eQTL Public
    immunogenomics/EarlyLate_RNA_eQTL’s past year of commit activity
    R 0 GPL-3.0 0 0 0 Updated Feb 18, 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 20 MIT 3 1 1 Updated Feb 3, 2025
  • TiRP Public

    code repository for Lagattuta et al. "Repertoire analyses reveal T cell receptor sequence features that influence T cell fate." Nat. Imm. (2022)

    immunogenomics/TiRP’s past year of commit activity
    Jupyter Notebook 12 GPL-3.0 5 1 0 Updated Jan 28, 2025
  • starCAT_website Public
    immunogenomics/starCAT_website’s past year of commit activity
    HTML 0 GPL-3.0 0 0 0 Updated Jan 6, 2025
  • crescendo Public

    Crescendo for single-gene correction in single-cell RNA-sequencing data

    immunogenomics/crescendo’s past year of commit activity
    R 5 1 1 0 Updated Dec 10, 2024
  • tcrpheno_analysis Public

    Code for analysis of TCR and T cell state data in Lagattuta, et al. Cell Reports 2025

    immunogenomics/tcrpheno_analysis’s past year of commit activity
    R 0 MIT 1 0 0 Updated Nov 24, 2024
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