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  1. harmony harmony Public

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

    R 491 95

  2. presto presto Public

    Fast Wilcoxon and auROC

    Jupyter Notebook 130 32

  3. symphony symphony Public

    Efficient and precise single-cell reference atlas mapping with Symphony

    Jupyter Notebook 92 22

  4. LISI LISI Public

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

    R 52 4

  5. cna cna Public

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

    Python 45 5

  6. HLA-TAPAS HLA-TAPAS Public

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

    Jupyter Notebook 43 17

Repositories

Showing 10 of 64 repositories
  • 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

    Jupyter Notebook 1 GPL-3.0 1 0 0 Updated Apr 19, 2024
  • minecraft-seq Public

    Code for analysis of MINECRAFT-seq data

    Jupyter Notebook 0 0 0 0 Updated Apr 5, 2024
  • PAUSE_eQTL Public

    Code for dynamic eQTL analysis of PAUSE trial

    R 1 GPL-3.0 1 0 0 Updated Mar 20, 2024
  • presto Public

    Fast Wilcoxon and auROC

    Jupyter Notebook 130 32 16 1 Updated Mar 18, 2024
  • reQTL Public

    Mapping of response eQTL in single cells

    R 0 0 0 0 Updated Mar 8, 2024
  • RA_Atlas_CITEseq Public

    RA Synovial Single-cell Multimodal Cell Atlas

    Jupyter Notebook 8 1 0 0 Updated Mar 6, 2024
  • harmony Public

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

    R 491 95 66 2 Updated Feb 3, 2024
  • scHLApers Public

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

    Jupyter Notebook 16 GPL-3.0 1 1 0 Updated Jan 10, 2024
  • SCENT Public

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

    R 36 5 3 0 Updated Jan 2, 2024
  • HLA-TAPAS Public

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

    Jupyter Notebook 43 17 14 1 Updated Dec 19, 2023