Software

Computational Biomedicine Group

Computational tools

omnideconv

R package for bulk RNA-seq decon volution informed by single-cell RNA-seq atlases

Code and documentation

SimBu

Bias-aware simulator of pseudo-bulk RNA-seq data with variable cell-type composition

Code and documentation

nextNEOpi

Comprehensive and fully-automated bioinformatic pipeline to predict tumor neoantigens from raw DNA and RNA sequencing data.

Code and documentation

quanTIseq

Computational pipeline for the quantification of the Tumor Immune contexture from human RNA-seq data via deoncvolution.

Code and documentation

Scirpy

Scalable python-toolkit to analyse T cell receptor (TCR) or B cell receptor (BCR) repertoires from single-cell RNA sequencing (scRNA-seq) data.

Code and documentation

immunedeconv

R package for unified access to computational methods for estimating immune cell fractions from bulk RNA sequencing data.

Code and documentation

NeoFuse

User-friendly pipeline for the prediction of fusion neoantigens from tumor RNA sequencing data.

Code and documentation