Repositories list

• MixTCRclean

  Public
  Tool to detect putative issues in TCR sequences data

  R

  •

  Other

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 22, 2026Jul 22, 2026

• MixTCRviz

  Public
  Visualisation tool for repertoires of epitope-specific TCRs

  R

  •

  Other

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 22, 2026Jul 22, 2026

• MixMHC2pred

  Public
  HLA-II ligand predictor.

  t-cellhlamhc-binding-prediction

  t-cellhlamhc-binding-prediction

  C++

  •

  Other

  •1212 forks•4949 stars•00 issues•00 pull requests•Updated Jul 17, 2026Jul 17, 2026

• SuperCellMultiomicsAnalyses

  Public
  Analysis of single-cell multiomics datasets using metacell tools

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 6, 2026Jul 6, 2026

• TEMPO

  Public
  TCR-epitope motif-based interaction predictor

  Other

  •00 forks•22 stars•00 issues•00 pull requests•Updated Jun 24, 2026Jun 24, 2026

• ggseqlogo

  Public
  Publication-quality sequence logos in R

  R

  •3232 forks•11 star•00 issues•00 pull requests•Updated Apr 27, 2026Apr 27, 2026

• SuperCell

  Public
  Coarse-graining of large single-cell RNA-seq data into metacells

  r-packagescrna-seq-datacoarse-graining+ 1

  r-packagescrna-seq-datacoarse-grainingscrna-seq-analysis

  R

  •

  GNU General Public License v3.0

  •1616 forks•104104 stars•55 issues•22 pull requests•Updated Apr 16, 2026Apr 16, 2026

• MixMHCpred

  Public
  HLA-I ligand predictor

  Python

  •

  Other

  •1111 forks•4646 stars•11 issue•00 pull requests•Updated Mar 19, 2026Mar 19, 2026

• SuperCellMultiomicsHTAN

  Public
  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 12, 2026Feb 12, 2026

• TANs_ATACseq_analyses

  Public
  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 9, 2026Feb 9, 2026

• SuperSpot

  Public
  HTML

  •00 forks•33 stars•11 issue•00 pull requests•Updated Nov 6, 2025Nov 6, 2025

• MixTCRcross

  Public
  Predictor of TCR cross-reactivity between a pair of epitopes

  R

  •

  Other

  •00 forks•11 star•00 issues•00 pull requests•Updated Oct 9, 2025Oct 9, 2025

• PRIME

  Public
  PRedictor of IMmunogenic Epitopes

  C++

  •

  Other

  •55 forks•3434 stars•00 issues•00 pull requests•Updated Sep 24, 2025Sep 24, 2025

• MixTCRpred

  Public
  Predictor of TCR-epitope interactions

  Python

  •

  Other

  •1010 forks•3838 stars•11 issue•00 pull requests•Updated Sep 9, 2025Sep 9, 2025

• MoDec

  Public
  Tool for Motif Deconvolution in large HLA-II ligand datasets without the need of prior alignment.

  mhchladeconvolution

  mhchladeconvolution

  R

  •

  Other

  •11 fork•1515 stars•00 issues•00 pull requests•Updated Feb 17, 2025Feb 17, 2025

• EPIC-ATAC_manuscript

  Public
  Code used for the analyses performed in the EPIC-ATAC manuscript

  R

  •

  Other

  •00 forks•33 stars•00 issues•00 pull requests•Updated Oct 8, 2024Oct 8, 2024

• EPIC-ATAC

  Public
  R

  •

  Other

  •00 forks•11 star•11 issue•00 pull requests•Updated Oct 1, 2024Oct 1, 2024

• MetacellAnalysisToolkit

  Public
  Toolkit for metacell analysis

  R

  •55 forks•2424 stars•33 issues•00 pull requests•Updated Aug 8, 2024Aug 8, 2024

• MetacellAnalysisTutorial

  Public
  Tutorial on construction and analysis of metacells

  TeX

  •00 forks•99 stars•00 issues•00 pull requests•Updated Mar 7, 2024Mar 7, 2024

• MixMHCp

  Public
  Tool for motif deconvolution in large HLA-I ligand datasets

  R

  •

  Other

  •22 forks•1010 stars•00 issues•00 pull requests•Updated Oct 6, 2023Oct 6, 2023

• EPIC

  Public
  Repository for the R package EPIC, to Estimate the Proportion of Immune and Cancer cells from bulk gene expression data.

  rna-seqgene-expressionbulk-data+ 2

  rna-seqgene-expressionbulk-datacell-typecancer-cells

  R

  •

  Other

  •2222 forks•8787 stars•00 issues•00 pull requests•Updated Jul 12, 2023Jul 12, 2023

• SIB_workshop

  Public
  Jupyter Notebook

  •00 forks•55 stars•00 issues•00 pull requests•Updated Jun 15, 2022Jun 15, 2022

• PLDpred

  Public
  Predictions of peptide length distribution for HLA-I molecules

  R

  •00 forks•11 star•00 issues•00 pull requests•Updated Oct 1, 2020Oct 1, 2020

• PhosMHCpred

  Public
  Predictor of Phosphorylated HLA-I ligands

  Python

  •22 forks•55 stars•00 issues•00 pull requests•Updated Jun 30, 2020Jun 30, 2020

• MHCpExt

  Public
  Identification of N- and C-terminal extensions in HLA-I ligands

  Perl

  •

  Other

  •22 forks•22 stars•00 issues•00 pull requests•Updated May 4, 2018May 4, 2018

• DCApeptides

  Public
  Extension of Direct Coupling Analysis to consider multiple ligands

  C++

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 25, 2017Aug 25, 2017