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  1. harmony harmony Public

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

    R 501 95

  2. presto presto Public

    Fast Wilcoxon and auROC

    Jupyter Notebook 141 33

  3. symphony symphony Public

    Efficient and precise single-cell reference atlas mapping with Symphony

    Jupyter Notebook 94 22

  4. LISI LISI Public

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

    R 54 5

  5. SCENT SCENT Public

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

    R 49 6

  6. 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 47 10

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  • 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 1 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
  • SCENT Public

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

    immunogenomics/SCENT’s past year of commit activity
    R 49 6 1 0 Updated May 28, 2024
  • presto Public

    Fast Wilcoxon and auROC

    immunogenomics/presto’s past year of commit activity
    Jupyter Notebook 141 33 17 1 Updated May 22, 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 8 MIT 1 0 0 Updated May 21, 2024
  • TB-g2g Public

    Code for genome-to-genome study of tuberculosis

    immunogenomics/TB-g2g’s past year of commit activity
    Jupyter Notebook 0 GPL-3.0 1 0 0 Updated May 20, 2024
  • TCAT_analysis Public

    Code repository for TCAT analyses

    immunogenomics/TCAT_analysis’s past year of commit activity
    Jupyter Notebook 4 2 0 0 Updated May 6, 2024
  • 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 Apr 5, 2024
  • PAUSE_eQTL Public

    Code for dynamic eQTL analysis of PAUSE trial

    immunogenomics/PAUSE_eQTL’s past year of commit activity
    R 1 GPL-3.0 1 0 0 Updated Mar 20, 2024
  • reQTL Public

    Mapping of response eQTL in single cells

    immunogenomics/reQTL’s past year of commit activity
    R 0 0 0 0 Updated Mar 8, 2024

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