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An open API service indexing awesome lists of open source software.

Projects in Awesome Lists by immunogenomics

A curated list of projects in awesome lists by immunogenomics .

https://github.com/immunogenomics/harmony

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

algorithm data-integration r scrna-seq

Last synced: 11 May 2025

https://github.com/immunogenomics/presto

Fast Wilcoxon and auROC

Last synced: 27 Jun 2025

https://github.com/immunogenomics/symphony

Efficient and precise single-cell reference atlas mapping with Symphony

bioinfo mapping r scrna-seq

Last synced: 28 Jun 2025

https://github.com/immunogenomics/scent

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

Last synced: 08 Jul 2025

https://github.com/immunogenomics/hla_analyses_tutorial

A thorough tutorial on HLA imputation and association, accompanying our manuscript "Tutorial: A statistical genetics guide to identifying HLA alleles driving complex disease"

Last synced: 27 Jun 2025

https://github.com/immunogenomics/lisi

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

Last synced: 12 Jul 2025

https://github.com/immunogenomics/hla-tapas

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

Last synced: 27 Jun 2025

https://github.com/immunogenomics/cna

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

python single-cell

Last synced: 07 May 2025

https://github.com/immunogenomics/starcat

Implements *CellAnnotator (aka *CAT/starCAT), annotating scRNA-Seq with predefined gene expression programs

Last synced: 28 Jun 2025

https://github.com/immunogenomics/sceqtl

Code for single-cell eQTL analysis of memory T cell data in Nathan, et al. bioRxiv (2021)

Last synced: 27 Jun 2025

https://github.com/immunogenomics/ra_atlas_citeseq

RA Synovial Single-cell Multimodal Cell Atlas

Last synced: 12 Oct 2025

https://github.com/immunogenomics/impact

Code for creating cell-type-specific regulatory element annotation files

Last synced: 29 Oct 2025

https://github.com/immunogenomics/schlapers

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

alignment expression hla single-cell

Last synced: 05 Oct 2025

https://github.com/immunogenomics/gena

Genotype-Neighborhood Associations: A tool for identifying genetic variant associations to the abundance of cell states in single-cell datasets

Last synced: 25 Oct 2025

https://github.com/immunogenomics/goshifter

GoShifter

Last synced: 12 Aug 2025

https://github.com/immunogenomics/ra_gwas

Trans-ancestry GWAS of rheumatoid arthritis

Last synced: 03 Jul 2025

https://github.com/immunogenomics/tb_tcell_citeseq

Code for analysis of memory T cell CITE-seq data

Last synced: 18 Aug 2025

https://github.com/immunogenomics/notch

Code to reproduce analyses and figures for manuscript: "Synovial fibroblast positional identity controlled by inductive Notch signaling underlies pathologic damage in inflammatory arthritis"

Last synced: 27 Jun 2025

https://github.com/immunogenomics/crescendo

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

Last synced: 27 Jun 2025

https://github.com/immunogenomics/fibroblastatlas

The Fibroblast Atlas

Last synced: 07 Aug 2025

https://github.com/immunogenomics/deeplearning_fan

:desktop_computer: Implement deep learning methods in the single-cell world.

Last synced: 29 Jan 2026

https://github.com/immunogenomics/amp_phase1_ra_viewer

🌻 View single-cell RNA-seq and mass cytometry data in synovial tissues from patients with RA or OA.

cytof-data data-science data-visualization r rna-seq-data shiny-apps single-cell-rna-seq

Last synced: 27 Jun 2025

https://github.com/immunogenomics/itcviewer

:rainbow: Innate T Cell RNA-seq data viewer.

r rna-seq visualization

Last synced: 14 Oct 2025

https://github.com/immunogenomics/ra_ipf_cellatlas

Visualize multiple lung phenotypes (RA-ILD, IPF, other) by single-cell

Last synced: 08 Sep 2025

https://github.com/immunogenomics/ra_atac_multiome

Code corresponding to Weinand et al., The chromatin landscape of pathogenic transcriptional cell states in rheumatoid arthritis, Nature Communications, 2024

Last synced: 22 Jul 2025

https://github.com/immunogenomics/gena-applied

Code and analyses supporting the GeNA single-cell csaQTL manuscript.

Last synced: 25 Feb 2026

https://github.com/immunogenomics/snatac_benchmark

Code corresponding to Weinand et al., Defining effective strategies to integrate multi-sample single-nucleus ATAC-seq datasets via a multimodal-guided approach, Submitted.

Last synced: 27 Jun 2025

https://github.com/immunogenomics/scpower

single cell power analysis

Last synced: 27 Jun 2025

https://github.com/immunogenomics/summerofcode

Resources for Summer of Code '19

Last synced: 27 Jun 2025

https://github.com/immunogenomics/ttek

TteK (Granzyme K+ CD8 T cells): the core population of inflamed human tissue-associated CD8 T cells

Last synced: 14 Oct 2025

https://github.com/immunogenomics/eqtl_kathryn

Kathryn's summer project with the Raychaudhuri Lab June-August 2019

Last synced: 02 Aug 2025

https://github.com/immunogenomics/amp_sle_kidney

Scripts for AMP_SLE_Kidney

Last synced: 07 Oct 2025

https://github.com/immunogenomics/reqtl

Mapping of response eQTL in single cells

Last synced: 27 Jun 2025

https://github.com/immunogenomics/tb-g2g

Code for genome-to-genome study of tuberculosis

Last synced: 27 Jun 2025

https://github.com/immunogenomics/summerofcodegit

Test repo for learning git

Last synced: 13 Feb 2026

https://github.com/immunogenomics/itc

Scripts to analyze innate T cell transcriptomes

Last synced: 27 Jun 2025

https://github.com/immunogenomics/cna-sim

Simulation code for CNA evaluation

Last synced: 28 Jun 2025