ICBI 's repositories
infercnvpy
Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
atlas_protocol
A computational protocol for atlas-level data integration and analysis as performed in Salcher et al. (2022).
hairy_cell_leukemia
Single-cell analysis of Hairy Cell Leukemia samples published in Bohn et al.
loncova_mcb_2024
Code to for the MCB chapter in "Immuno-oncology and immunotherapy" (Loncova et al. 2024)
plattner_mcb_2024
Code for the MCB chapter in "Immuno-oncology and immunotherapy" (Plattner et al. 2024)
hgsoc
Code Repository for 'Integrated immunogenomic analyses of high-grade serous ovarian cancer reveal vulnerability to combination immunotherapy'
plattner_2023
Code to reproduce figures from Plattner et al. (2022)
icbi-lab.github.io
For now, redirect to ICBI website.
downloader
Easy & parallel download of FASTQ files from public repositories (SRA, EGA, GDC)
deseq2icbi
R script to perform DE and Pathway enrichment analysis based on the output of nf-core/rnaseq
bioconda-recipes
Conda recipes for the bioconda channel.
duurland2021_paper
Single-cell analysis for Duurland et al.
abdulrahman2021_paper
single-cell analysis for the Abdulrahman et al. (2021) paper.
cellxgene-user-guide
Step-by-step instructions how to use the cell-x-gene portal
kortekaas2020_paper
Single cell RNA-seq analysis accompanying Kortekaas, Santegoets et al. (2020)