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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 545 101

  2. presto presto Public

    Fast Wilcoxon and auROC

    Jupyter Notebook 172 36

  3. symphony symphony Public

    Efficient and precise single-cell reference atlas mapping with Symphony

    Jupyter Notebook 102 23

  4. SCENT SCENT Public

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

    R 69 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 64 13

  6. LISI LISI Public

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

    R 60 5

Repositories

Showing 10 of 67 repositories
  • 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 Jan 31, 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
  • TCAT_analysis Public

    Code repository for TCAT analyses

    immunogenomics/TCAT_analysis’s past year of commit activity
    Jupyter Notebook 7 2 0 0 Updated Jan 13, 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 1 1 1 0 Updated Dec 10, 2024
  • tcrpheno_analysis Public

    Code for analysis of TCR and T cell state data in Lagattuta, et al. bioRxiv (2023)

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

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

    immunogenomics/harmony’s past year of commit activity
    R 545 101 75 2 Updated Nov 11, 2024
  • presto Public

    Fast Wilcoxon and auROC

    immunogenomics/presto’s past year of commit activity
    Jupyter Notebook 172 36 17 1 Updated Nov 8, 2024
  • 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 Oct 25, 2024
  • 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 47 GPL-3.0 5 0 0 Updated Oct 24, 2024
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