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    68 repositories

    • craft-seq

      Public
      Code for analysis of CRAFT-seq data
      Jupyter Notebook
      •0•1•0•0•Updated May 15, 2025May 15, 2025

    • 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•50•0•0•Updated May 12, 2025May 12, 2025

    • starCAT

      Public
      Implements *CellAnnotator (aka *CAT/starCAT), annotating scRNA-Seq with predefined gene expression programs
      Jupyter Notebook
      •
      MIT License
      •3•23•0•1•Updated Apr 29, 2025Apr 29, 2025

    • 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 Apr 29, 2025Apr 29, 2025

    • cna-display

      Public
      Generation of display items for CNA paper
      Jupyter Notebook
      •
      MIT License
      •1•3•0•0•Updated Apr 28, 2025Apr 28, 2025

    • cna-sim

      Public
      Simulation code for CNA evaluation
      Python
      •
      GNU General Public License v3.0
      •0•0•1•0•Updated Apr 28, 2025Apr 28, 2025

    • SCENT

      Public
      Single-Cell ENhancer Target gene mapping using multimodal data with ATAC + RNA
      R
      •
      Other
      •11•74•1•0•Updated Apr 21, 2025Apr 21, 2025

    • snATAC_benchmark

      Public
      Code corresponding to Weinand et al., Defining effective strategies to integrate multi-sample single-nucleus ATAC-seq datasets via a multimodal-guided approach, Submitted.
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•1•0•0•Updated Apr 8, 2025Apr 8, 2025

    • TCAT_analysis

      Public
      Code repository for TCAT analyses
      Jupyter Notebook
      •2•7•0•0•Updated Mar 13, 2025Mar 13, 2025

    • amp_phase1_ra

      Public
      🌾 Zhang, et al, Nature Immunology, 2019. Use single-cell transcriptomics and proteomics to study autoimmune diseases.
      rjupyter-notebookautoimmunesingle-cell-genomicssingle-cell-proteomicsimmunogenomics
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •13•20•1•0•Updated Mar 11, 2025Mar 11, 2025

    • EarlyLate_RNA_eQTL

      Public
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Feb 18, 2025Feb 18, 2025

    • TiRP

      Public
      code repository for Lagattuta et al. "Repertoire analyses reveal T cell receptor sequence features that influence T cell fate." Nat. Imm. (2022)
      tcrsingle-cellsequence-analysismixed-effects-modelstreg
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •5•13•1•0•Updated Jan 28, 2025Jan 28, 2025

    • starCAT_website

      Public
      HTML
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jan 6, 2025Jan 6, 2025

    • crescendo

      Public
      Crescendo for single-gene correction in single-cell RNA-sequencing data
      R
      •
      Other
      •1•5•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. Cell Reports 2025
      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
      •102•573•77•2•Updated Nov 11, 2024Nov 11, 2024

    • presto

      Public
      Fast Wilcoxon and auROC
      Jupyter Notebook
      •36•181•18•1•Updated Nov 8, 2024Nov 8, 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
      •14•67•1•0•Updated Oct 10, 2024Oct 10, 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•14•0•0•Updated Oct 5, 2024Oct 5, 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

    • 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

    • 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•14•1•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
      •23•53•16•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•5•0•0•Updated Oct 14, 2023Oct 14, 2023