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@GfellerLab Cancer Immune Recognition Lab

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    25 repositories

    • MixMHCpred

      Public
      HLA-I ligand predictor
      Python
      •
      Other
      •10•45•1•1•Updated Mar 19, 2026Mar 19, 2026

    • SuperCell

      Public
      Coarse-graining of large single-cell RNA-seq data into metacells
      r-packagescrna-seq-datacoarse-graining
      r-packagescrna-seq-datacoarse-grainingscrna-seq-analysis
      R
      •
      GNU General Public License v3.0
      •15•99•5•2•Updated Feb 23, 2026Feb 23, 2026

    • SuperCellMultiomicsHTAN

      Public
      R
      •0•0•0•0•Updated Feb 12, 2026Feb 12, 2026

    • SuperCellMultiomicsAnalyses

      Public
      Analysis of single-cell multiomics datasets using metacell tools
      MIT License
      •0•0•0•0•Updated Feb 12, 2026Feb 12, 2026

    • TANs_ATACseq_analyses

      Public
      R
      •0•0•0•0•Updated Feb 9, 2026Feb 9, 2026

    • MixTCRclean

      Public
      Tool to detect putative issues in TCR sequences data
      R
      •
      Other
      •0•0•0•0•Updated Dec 9, 2025Dec 9, 2025

    • TEMPO

      Public
      TCR-epitope motif-based interaction predictor
      Other
      •0•1•1•0•Updated Nov 13, 2025Nov 13, 2025

    • SuperSpot

      Public
      HTML
      •0•3•1•0•Updated Nov 6, 2025Nov 6, 2025

    • MixTCRcross

      Public
      Predictor of TCR cross-reactivity between a pair of epitopes
      R
      •
      Other
      •0•0•0•0•Updated Oct 9, 2025Oct 9, 2025

    • PRIME

      Public
      PRedictor of IMmunogenic Epitopes
      C++
      •
      Other
      •4•29•0•0•Updated Sep 24, 2025Sep 24, 2025

    • MixTCRpred

      Public
      Predictor of TCR-epitope interactions
      Python
      •
      Other
      •10•34•1•0•Updated Sep 9, 2025Sep 9, 2025

    • ggseqlogo

      Public
      Publication-quality sequence logos in R
      R
      •32•1•0•0•Updated Feb 20, 2025Feb 20, 2025

    • MoDec

      Public
      Tool for Motif Deconvolution in large HLA-II ligand datasets without the need of prior alignment.
      mhchladeconvolution
      mhchladeconvolution
      R
      •
      Other
      •1•15•0•0•Updated Feb 17, 2025Feb 17, 2025

    • EPIC-ATAC_manuscript

      Public
      Code used for the analyses performed in the EPIC-ATAC manuscript
      R
      •
      Other
      •0•3•0•0•Updated Oct 8, 2024Oct 8, 2024

    • EPIC-ATAC

      Public
      R
      •
      Other
      •0•1•0•0•Updated Oct 1, 2024Oct 1, 2024

    • MetacellAnalysisToolkit

      Public
      Toolkit for metacell analysis
      R
      •5•23•3•0•Updated Aug 8, 2024Aug 8, 2024

    • MetacellAnalysisTutorial

      Public
      Tutorial on construction and analysis of metacells
      TeX
      •0•9•0•0•Updated Mar 7, 2024Mar 7, 2024

    • MixMHCp

      Public
      Tool for motif deconvolution in large HLA-I ligand datasets
      R
      •
      Other
      •2•10•0•0•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
      rna-seqgene-expressionbulk-datacell-typecancer-cells
      R
      •
      Other
      •22•85•0•0•Updated Jul 12, 2023Jul 12, 2023

    • MixMHC2pred

      Public
      HLA-II ligand predictor.
      t-cellhlamhc-binding-prediction
      t-cellhlamhc-binding-prediction
      C++
      •
      Other
      •11•45•1•0•Updated Apr 6, 2023Apr 6, 2023

    • SIB_workshop

      Public
      Jupyter Notebook
      •0•5•0•0•Updated Jun 15, 2022Jun 15, 2022

    • PLDpred

      Public
      Predictions of peptide length distribution for HLA-I molecules
      R
      •0•1•0•0•Updated Oct 1, 2020Oct 1, 2020

    • PhosMHCpred

      Public
      Predictor of Phosphorylated HLA-I ligands
      Python
      •2•5•0•0•Updated Jun 30, 2020Jun 30, 2020

    • MHCpExt

      Public
      Identification of N- and C-terminal extensions in HLA-I ligands
      Perl
      •
      Other
      •2•2•0•0•Updated May 4, 2018May 4, 2018

    • DCApeptides

      Public
      Extension of Direct Coupling Analysis to consider multiple ligands
      C++
      •0•0•0•0•Updated Aug 25, 2017Aug 25, 2017
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