ICBI

infercnvpy

Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.

nextNEOpi

nextNEOpi: a comprehensive pipeline for computational neoantigen prediction

luca

Single-cell Lung Cancer Atlas with 1.2M cells

quanTIseq

a computational pipeline for the quantification of the Tumor Immune contexture from human RNA-seq data

NeoFuse

NeoFuse is a user-friendly pipeline for the prediction of fusion neoantigens from tumor RNA-seq data.

downloader

Easy & parallel download of FASTQ files from public repositories (SRA, EGA, GDC)

current-topics-bioinformatics-lecture

atlas_protocol

A computational protocol for atlas-level data integration and analysis as performed in Salcher et al. (2022).

nf-deseq2

A RNA-seq differential expression analysis pipeline downstream of nf-core/rnaseq.

meRanTK

methylated RNA Tool Kit

nmp-liver

Single cell analysis of donor livers pre- and post machine perfusion

deseq2icbi

R script to perform DE and Pathway enrichment analysis based on the output of nf-core/rnaseq

DoseRider

DoseRider: Generalized Additive Mixed Models (GAMMs) for Analyzing Dose-Response Relationships in Gene Expression Data

abdulrahman2021_paper

single-cell analysis for the Abdulrahman et al. (2021) paper.

borst2021

single-cell analysis for the Borst et al. (2021) paper.

duurland2021_paper

Single-cell analysis for Duurland et al.

kortekaas2020_paper

Single cell RNA-seq analysis accompanying Kortekaas, Santegoets et al. (2020)

miopy

OvRSeq

OvRSeq is an R package for analyzing RNA sequencing data from ovarian cancer patients.

plattner_2023

Code to reproduce figures from Plattner et al. (2022)

bioconda-recipes

Conda recipes for the bioconda channel.

cellxgene-user-guide

Step-by-step instructions how to use the cell-x-gene portal

hairy_cell_leukemia

Single-cell analysis of Hairy Cell Leukemia samples published in Bohn et al.

hgsoc

Code Repository for 'Integrated immunogenomic analyses of high-grade serous ovarian cancer reveal vulnerability to combination immunotherapy'

icbi-lab.github.io

For now, redirect to ICBI website.

indelicato_2023

kirchmair_2023

loncova_mcb_2024

Code to for the MCB chapter in "Immuno-oncology and immunotherapy" (Loncova et al. 2024)

mio

plattner_mcb_2024

Code for the MCB chapter in "Immuno-oncology and immunotherapy" (Plattner et al. 2024)