Repositories list

• harmony

  Public

  immunogenomics/harmony’s past year of commit activity
  Fast, sensitive and accurate integration of single-cell data with Harmony

  algorithmrscrna-seq+ 1

  algorithmrscrna-seqdata-integration

  R

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  Other

  •105105 forks•640640 stars•8282 issues•33 pull requests•Updated Apr 20, 2026Apr 20, 2026

• starCAT

  Public

  immunogenomics/starCAT’s past year of commit activity
  Implements *CellAnnotator (aka *CAT/starCAT), annotating scRNA-Seq with predefined gene expression programs

  Jupyter Notebook

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  MIT License

  •55 forks•100100 stars•66 issues•22 pull requests•Updated Apr 8, 2026Apr 8, 2026

• EarlyLate_RNA_eQTL

  Public

  immunogenomics/EarlyLate_RNA_eQTL’s past year of commit activity
  R

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  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 11, 2026Mar 11, 2026

• starCAT_website

  Public

  immunogenomics/starCAT_website’s past year of commit activity
  HTML

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  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 9, 2025Nov 9, 2025

• symphony

  Public

  immunogenomics/symphony’s past year of commit activity
  Efficient and precise single-cell reference atlas mapping with Symphony

  rmappingscrna-seq+ 1

  rmappingscrna-seqbioinfo

  Jupyter Notebook

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  GNU General Public License v3.0

  •2323 forks•117117 stars•1717 issues•00 pull requests•Updated Oct 31, 2025Oct 31, 2025

• TCAT_analysis

  Public

  immunogenomics/TCAT_analysis’s past year of commit activity
  Code repository for TCAT analyses

  Jupyter Notebook

  •22 forks•1414 stars•00 issues•00 pull requests•Updated Sep 26, 2025Sep 26, 2025

• AMP_SLE_Kidney

  Public

  immunogenomics/AMP_SLE_Kidney’s past year of commit activity
  Scripts for AMP_SLE_Kidney

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 9, 2025Sep 9, 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

  pythonsingle-cell

  Python

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  GNU General Public License v3.0

  •55 forks•5757 stars•00 issues•00 pull requests•Updated Jun 1, 2025Jun 1, 2025

• craft-seq

  Public

  immunogenomics/craft-seq’s past year of commit activity
  Code for analysis of CRAFT-seq data

  Jupyter Notebook

  •00 forks•22 stars•00 issues•00 pull requests•Updated May 15, 2025May 15, 2025

• GeNA-applied

  Public

  immunogenomics/GeNA-applied’s past year of commit activity
  Code and analyses supporting the GeNA single-cell csaQTL manuscript.

  Jupyter Notebook

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  GNU General Public License v3.0

  •00 forks•22 stars•00 issues•00 pull requests•Updated Apr 29, 2025Apr 29, 2025

• cna-display

  Public
  Generation of display items for CNA paper

  Jupyter Notebook

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  MIT License

  •11 fork•33 stars•00 issues•00 pull requests•Updated Apr 28, 2025Apr 28, 2025

• cna-sim

  Public
  Simulation code for CNA evaluation

  Python

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  GNU General Public License v3.0

  •00 forks•00 stars•11 issue•00 pull requests•Updated Apr 28, 2025Apr 28, 2025

• SCENT

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

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  Other

  •1111 forks•8585 stars•11 issue•00 pull requests•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,…

  Jupyter Notebook

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  GNU General Public License v3.0

  •11 fork•11 star•00 issues•00 pull requests•Updated Apr 8, 2025Apr 8, 2025

• amp_phase1_ra

  Public
  :ear_of_rice: Zhang, et al, Nature Immunology, 2019. Use single-cell transcriptomics and proteomics to study autoimmune diseases.

  rjupyter-notebookautoimmune+ 3

  rjupyter-notebookautoimmunesingle-cell-genomicssingle-cell-proteomicsimmunogenomics

  Jupyter Notebook

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  GNU General Public License v3.0

  •1313 forks•2121 stars•11 issue•00 pull requests•Updated Mar 11, 2025Mar 11, 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-analysis+ 2

  tcrsingle-cellsequence-analysismixed-effects-modelstreg

  Jupyter Notebook

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  GNU General Public License v3.0

  •55 forks•1414 stars•11 issue•00 pull requests•Updated Jan 28, 2025Jan 28, 2025

• crescendo

  Public
  Crescendo for single-gene correction in single-cell RNA-sequencing data

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  Other

  •11 fork•77 stars•22 issues•00 pull requests•Updated Dec 10, 2024Dec 10, 2024

• tcrpheno_analysis

  Public

  immunogenomics/tcrpheno_analysis’s past year of commit activity
  Code for analysis of TCR and T cell state data in Lagattuta, et al. Cell Reports 2025

  R

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  MIT License

  •11 fork•00 stars•00 issues•00 pull requests•Updated Nov 24, 2024Nov 24, 2024

• presto

  Public
  Fast Wilcoxon and auROC

  Jupyter Notebook

  •4242 forks•207207 stars•1818 issues•22 pull requests•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 co…

  Jupyter Notebook

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  GNU General Public License v3.0

  •1313 forks•7373 stars•00 issues•00 pull requests•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

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  GNU General Public License v3.0

  •11 fork•1616 stars•00 issues•00 pull requests•Updated Oct 5, 2024Oct 5, 2024

• singlecellmethods

  Public
  Collection of useful methods for single cell analysis

  Jupyter Notebook

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  GNU General Public License v3.0

  •55 forks•1515 stars•11 issue•00 pull requests•Updated Aug 22, 2024Aug 22, 2024

• RA_ATAC_multiome

  Public

  immunogenomics/RA_ATAC_multiome’s past year of commit activity
  Code corresponding to Weinand et al., The chromatin landscape of pathogenic transcriptional cell states in rheumatoid arthritis, Nature Communications, 2024

  Jupyter Notebook

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  GNU General Public License v3.0

  •11 fork•22 stars•00 issues•00 pull requests•Updated Jun 24, 2024Jun 24, 2024

• IMPACT

  Public

  immunogenomics/IMPACT’s past year of commit activity
  Code for creating cell-type-specific regulatory element annotation files

  R

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  GNU General Public License v3.0

  •88 forks•2020 stars•11 issue•22 pull requests•Updated Jun 11, 2024Jun 11, 2024

• TB-g2g

  Public

  immunogenomics/TB-g2g’s past year of commit activity
  Code for genome-to-genome study of tuberculosis

  Jupyter Notebook

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  GNU General Public License v3.0

  •11 fork•00 stars•00 issues•00 pull requests•Updated May 20, 2024May 20, 2024

• PAUSE_eQTL

  Public
  Code for dynamic eQTL analysis of PAUSE trial

  R

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  GNU General Public License v3.0

  •11 fork•11 star•00 issues•00 pull requests•Updated Mar 20, 2024Mar 20, 2024

• reQTL

  Public
  Mapping of response eQTL in single cells

  R

  •00 forks•22 stars•00 issues•00 pull requests•Updated Mar 8, 2024Mar 8, 2024

• RA_Atlas_CITEseq

  Public
  RA Synovial Single-cell Multimodal Cell Atlas

  Jupyter Notebook

  •33 forks•2121 stars•11 issue•00 pull requests•Updated Mar 6, 2024Mar 6, 2024

• scHLApers

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

  expressionalignmentsingle-cell+ 1

  expressionalignmentsingle-cellhla

  Jupyter Notebook

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  GNU General Public License v3.0

  •11 fork•1717 stars•11 issue•00 pull requests•Updated Jan 10, 2024Jan 10, 2024

• HLA-TAPAS

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

  Jupyter Notebook

  •2424 forks•5555 stars•1919 issues•11 pull request•Updated Dec 19, 2023Dec 19, 2023