Computational Cancer Biology Lab

Computational Cancer Biology Lab's repositories

EPIC

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

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SuperCell

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

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MixMHC2pred

HLA-II ligand predictor.

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MixMHCpred

HLA-I ligand predictor

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PRIME

PRedictor of IMmunogenic Epitopes

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MixTCRpred

Predictor of TCR-epitope interactions

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MetacellAnalysisToolkit

Toolkit for metacell analysis

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MoDec

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

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MixMHCp

Tool for motif deconvolution in large HLA-I ligand datasets

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PhosMHCpred

Predictor of Phosphorylated HLA-I ligands

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MetacellAnalysisTutorial

Tutorial on construction and analysis of metacells

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SIB_workshop

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EPIC-ATAC

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ggseqlogo

Publication-quality sequence logos in R

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MHCpExt

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

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DCApeptides

Extension of Direct Coupling Analysis to consider multiple ligands

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EPIC-ATAC_manuscript

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

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exercises_intro_bioinfo_clinique

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PLDpred

Predictions of peptide length distribution for HLA-I molecules

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SuperSpot

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