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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 523 100

  2. presto presto Public

    Fast Wilcoxon and auROC

    Jupyter Notebook 161 35

  3. symphony symphony Public

    Efficient and precise single-cell reference atlas mapping with Symphony

    Jupyter Notebook 99 22

  4. SCENT SCENT Public

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

    R 65 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 57 5

Repositories

Showing 10 of 68 repositories
  • 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 16 MIT 2 0 0 Updated Oct 23, 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 45 GPL-3.0 5 0 0 Updated Oct 17, 2024
  • 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"

    immunogenomics/HLA_analyses_tutorial’s past year of commit activity
    Jupyter Notebook 59 GPL-3.0 12 0 0 Updated Oct 10, 2024
  • snATAC_benchmark Public

    Code corresponding to Weinand et al., Defining optimal strategies to integrate multi-sample single-nucleus ATAC-seq datasets via a multimodal-guided approach, In Prep.

    immunogenomics/snATAC_benchmark’s past year of commit activity
    R 0 GPL-3.0 0 0 0 Updated Oct 10, 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 11 GPL-3.0 1 1 0 Updated Oct 5, 2024
  • starCAT_website Public
    immunogenomics/starCAT_website’s past year of commit activity
    HTML 0 GPL-3.0 0 0 0 Updated Sep 26, 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 65 9 2 0 Updated Sep 4, 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
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