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    67 repositories

    • crescendo

      Public
      Crescendo for single-gene correction in single-cell RNA-sequencing data
      R
      •
      Other
      •1•1•1•0•Updated Dec 10, 2024Dec 10, 2024

    • tcrpheno_analysis

      Public
      Code for analysis of TCR and T cell state data in Lagattuta, et al. bioRxiv (2023)
      R
      •
      MIT License
      •1•0•0•0•Updated Nov 24, 2024Nov 24, 2024

    • harmony

      Public
      Fast, sensitive and accurate integration of single-cell data with Harmony
      algorithmrscrna-seqdata-integration
      R
      •
      Other
      •98•534•74•2•Updated Nov 11, 2024Nov 11, 2024

    • presto

      Public
      Fast Wilcoxon and auROC
      Jupyter Notebook
      •36•167•17•1•Updated Nov 8, 2024Nov 8, 2024

    • starCAT

      Public
      Implements *CellAnnotator (aka *CAT/starCAT), annotating scRNA-Seq with predefined gene expression programs
      Jupyter Notebook
      •
      MIT License
      •3•19•0•1•Updated Oct 25, 2024Oct 25, 2024

    • cna

      Public
      Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-cell datasets.
      pythonsingle-cell
      Python
      •
      GNU General Public License v3.0
      •5•47•0•0•Updated Oct 24, 2024Oct 24, 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"
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •12•61•1•0•Updated Oct 10, 2024Oct 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.
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 9, 2024Oct 9, 2024

    • GeNA

      Public
      Genotype-Neighborhood Associations: A tool for identifying genetic variant associations to the abundance of cell states in single-cell datasets
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•12•0•0•Updated Oct 5, 2024Oct 5, 2024

    • starCAT_website

      Public
      HTML
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 26, 2024Sep 26, 2024

    • SCENT

      Public
      Single-Cell ENhancer Target gene mapping using multimodal data with ATAC + RNA
      R
      •
      Other
      •9•67•2•0•Updated Sep 4, 2024Sep 4, 2024

    • singlecellmethods

      Public
      Collection of useful methods for single cell analysis
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •5•14•1•0•Updated Aug 22, 2024Aug 22, 2024

    • GeNA-applied

      Public
      Code and analyses supporting the GeNA single-cell csaQTL manuscript.
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated Aug 9, 2024Aug 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
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•2•0•0•Updated Jun 24, 2024Jun 24, 2024

    • IMPACT

      Public
      Code for creating cell-type-specific regulatory element annotation files
      R
      •
      GNU General Public License v3.0
      •8•18•1•2•Updated Jun 11, 2024Jun 11, 2024

    • TB-g2g

      Public
      Code for genome-to-genome study of tuberculosis
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated May 20, 2024May 20, 2024

    • TCAT_analysis

      Public
      Code repository for TCAT analyses
      Jupyter Notebook
      •2•7•0•0•Updated May 6, 2024May 6, 2024

    • minecraft-seq

      Public
      Code for analysis of MINECRAFT-seq data
      Jupyter Notebook
      •0•1•0•0•Updated Apr 5, 2024Apr 5, 2024

    • PAUSE_eQTL

      Public
      Code for dynamic eQTL analysis of PAUSE trial
      R
      •
      GNU General Public License v3.0
      •1•1•0•0•Updated Mar 20, 2024Mar 20, 2024

    • reQTL

      Public
      Mapping of response eQTL in single cells
      R
      •0•0•0•0•Updated Mar 8, 2024Mar 8, 2024

    • RA_Atlas_CITEseq

      Public
      RA Synovial Single-cell Multimodal Cell Atlas
      Jupyter Notebook
      •2•12•0•0•Updated Mar 6, 2024Mar 6, 2024

    • scHLApers

      Public
      Code to run the scHLApers pipeline for personalized single-cell HLA quantification
      expressionalignmentsingle-cellhla
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•17•1•0•Updated Jan 10, 2024Jan 10, 2024

    • HLA-TAPAS

      Public
      HLA-TAPAS pipeline for HLA association and fine-mapping studies
      Jupyter Notebook
      •21•49•15•1•Updated Dec 19, 2023Dec 19, 2023

    • mod-cna

      Public
      CNA package with the incorporation of modifications to illustrate and address confounding by cell count.
      Python
      •
      GNU General Public License v3.0
      •5•0•0•0•Updated Oct 19, 2023Oct 19, 2023

    • hla2023

      Public
      Code for mapping single-cell eQTLs for HLA genes across four cohorts
      Jupyter Notebook
      •0•4•0•0•Updated Oct 14, 2023Oct 14, 2023

    • sc-h2

      Public
      Jupyter Notebook
      •0•5•0•0•Updated Oct 12, 2023Oct 12, 2023

    • sceQTL

      Public
      Code for single-cell eQTL analysis of memory T cell data in Nathan, et al. bioRxiv (2021)
      R
      •
      GNU General Public License v3.0
      •2•15•0•0•Updated Jul 6, 2023Jul 6, 2023

    • 1K1K_QC

      Public
      Additional quality control applied to the published OneK1K dataset
      GNU General Public License v3.0
      •0•0•0•0•Updated Apr 11, 2023Apr 11, 2023

    • cdr3-QTL

      Public
      Trans-association between HLA and TCR-CDR3
      HTML
      •1•15•0•0•Updated Mar 29, 2023Mar 29, 2023

    • symphony

      Public
      Efficient and precise single-cell reference atlas mapping with Symphony
      rmappingscrna-seqbioinfo
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •22•100•15•0•Updated Feb 5, 2023Feb 5, 2023