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@immunogenomics

Raychaudhuri Lab

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  1. harmony harmony Public

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

    R 599 105

  2. presto presto Public

    Fast Wilcoxon and auROC

    Jupyter Notebook 188 35

  3. symphony symphony Public

    Efficient and precise single-cell reference atlas mapping with Symphony

    Jupyter Notebook 109 23

  4. SCENT SCENT Public

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

    R 77 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 69 12

  6. LISI LISI Public

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

    R 68 5

Repositories

Showing 10 of 69 repositories
  • AMP_SLE_Kidney Public

    Scripts for AMP_SLE_Kidney

    immunogenomics/AMP_SLE_Kidney’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Sep 9, 2025
  • starCAT_website Public
    immunogenomics/starCAT_website’s past year of commit activity
    HTML 0 GPL-3.0 0 0 0 Updated Sep 5, 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 53 MIT 3 5 1 Updated Aug 19, 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 55 GPL-3.0 5 0 0 Updated Jun 1, 2025
  • craft-seq Public

    Code for analysis of CRAFT-seq data

    immunogenomics/craft-seq’s past year of commit activity
    Jupyter Notebook 2 0 0 0 Updated May 15, 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 28, 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 27, 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 27, 2025
  • SCENT Public

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

    immunogenomics/SCENT’s past year of commit activity
    R 77 10 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
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