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@immunogenomics

Raychaudhuri Lab

Popular repositories

  1. harmony Public

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

    R 384 85

  2. presto Public

    Fast Wilcoxon and auROC

    R 92 22

  3. symphony Public

    Efficient and precise single-cell reference atlas mapping with Symphony

    Jupyter Notebook 80 18

  4. cna Public

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

    Python 36 4

  5. LISI Public

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

    R 34 3

  6. HLA-TAPAS Public

    HLA-TAPAS pipeline for HLA association and fine-mapping studies

    Jupyter Notebook 29 11

Repositories

  • cdr3-QTL Public

    Trans-association between HLA and TCR-CDR3

    HTML 14 1 0 0 Updated Mar 29, 2023
  • RA_ATAC_multiome Public

    Code corresponding to Weinand*, Sakaue* et al., The Chromatin Landscape of Pathogenic Transcriptional Cell States in Rheumatoid Arthritis, In Prep., 2023

    R 0 GPL-3.0 0 0 0 Updated Mar 28, 2023
  • harmony Public

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

    R 384 85 71 2 Updated Mar 22, 2023
  • SCENT Public

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

    R 15 4 1 0 Updated Mar 18, 2023
  • presto Public

    Fast Wilcoxon and auROC

    R 92 22 11 2 Updated Mar 16, 2023
  • scHLApers Public

    Code to run the scHLApers pipeline for personalized single-cell HLA quantification

    Jupyter Notebook 5 GPL-3.0 0 0 0 Updated Mar 9, 2023
  • sc-h2 Public
    Jupyter Notebook 0 0 0 0 Updated Mar 4, 2023
  • 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 15 GPL-3.0 2 1 0 Updated Feb 10, 2023
  • symphony Public

    Efficient and precise single-cell reference atlas mapping with Symphony

    Jupyter Notebook 80 GPL-3.0 18 11 0 Updated Feb 5, 2023
  • FibroblastAtlas2022 Public
    Jupyter Notebook 2 0 1 0 Updated Dec 6, 2022
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