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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 518 99

  2. presto presto Public

    Fast Wilcoxon and auROC

    Jupyter Notebook 156 34

  3. symphony symphony Public

    Efficient and precise single-cell reference atlas mapping with Symphony

    Jupyter Notebook 97 22

  4. SCENT SCENT Public

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

    R 64 9

  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 59 12

  6. LISI LISI Public

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

    R 56 5

Repositories

Showing 10 of 67 repositories
  • starCAT_website Public
    immunogenomics/starCAT_website’s past year of commit activity
    HTML 0 GPL-3.0 0 0 0 Updated Sep 26, 2024
  • GeNA Public

    Genotype-Neighborhood Associations: A tool for identifying genetic variant associations to the abundance of cell states in single-cell datasets

    immunogenomics/GeNA’s past year of commit activity
    Jupyter Notebook 9 GPL-3.0 0 0 0 Updated Sep 14, 2024
  • crescendo Public

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

    immunogenomics/crescendo’s past year of commit activity
    R 0 1 0 0 Updated Sep 13, 2024
  • SCENT Public

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

    immunogenomics/SCENT’s past year of commit activity
    R 64 9 3 0 Updated Sep 4, 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 14 MIT 2 0 0 Updated Aug 26, 2024
  • singlecellmethods Public

    Collection of useful methods for single cell analysis

    immunogenomics/singlecellmethods’s past year of commit activity
    Jupyter Notebook 14 GPL-3.0 5 1 0 Updated Aug 22, 2024
  • GeNA-applied Public

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

    immunogenomics/GeNA-applied’s past year of commit activity
    Jupyter Notebook 1 GPL-3.0 0 0 0 Updated Aug 9, 2024
  • RA_ATAC_multiome Public

    Code corresponding to Weinand et al., The chromatin landscape of pathogenic transcriptional cell states in rheumatoid arthritis, Nature Communications, 2024

    immunogenomics/RA_ATAC_multiome’s past year of commit activity
    Jupyter Notebook 2 GPL-3.0 1 0 0 Updated Jun 24, 2024
  • IMPACT Public

    Code for creating cell-type-specific regulatory element annotation files

    immunogenomics/IMPACT’s past year of commit activity
    R 18 GPL-3.0 8 1 2 Updated Jun 11, 2024
  • presto Public

    Fast Wilcoxon and auROC

    immunogenomics/presto’s past year of commit activity
    Jupyter Notebook 156 34 17 1 Updated May 22, 2024
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