Software

Rectangle

Python package to perform robust cell-type deconvolution informed by single-cell RNA-seq data

Code & Documentation

omnideconv

Ecosystem of tools and resources for single-cell-informed deconvolution of bulk RNA-seq data

Code & Documentation

spacedeconv

R package for the deconvolution of tissue architecture from spatial transcriptomics data

Code & Documentation

SimBu

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

Code & Documentation

immunedeconv

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

Code & Documentation

novumRNA

Next-flow pipeline for the computational prediction of non-canonical neoantigens

Code & Documentation

quanTIseq

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

Code & 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 & Documentation

nextNEOpi

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

Code & Documentation

NeoFuse

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

Code & Documentation