Pinned Repositories
downloader
Easy & parallel download of FASTQ files from public repositories (SRA, EGA, GDC)
IHCount
IHC-image analysis workflow
immune_deconvolution_benchmark
Reproducible pipeline for "Comprehensive evaluation of cell-type quantification methods for immuno-oncology", Sturm et al. 2019, https://doi.org/10.1093/bioinformatics/btz363
Immunophenogram
infercnvpy
Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
luca
Single-cell Lung Cancer Atlas with 1.2M cells
miopy
NeoFuse
NeoFuse is a user-friendly pipeline for the prediction of fusion neoantigens from tumor RNA-seq data.
nextNEOpi
nextNEOpi: a comprehensive pipeline for computational neoantigen prediction
quanTIseq
a computational pipeline for the quantification of the Tumor Immune contexture from human RNA-seq data
ICBI 's Repositories
icbi-lab/infercnvpy
Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
icbi-lab/nextNEOpi
nextNEOpi: a comprehensive pipeline for computational neoantigen prediction
icbi-lab/luca
Single-cell Lung Cancer Atlas with 1.2M cells
icbi-lab/quanTIseq
a computational pipeline for the quantification of the Tumor Immune contexture from human RNA-seq data
icbi-lab/NeoFuse
NeoFuse is a user-friendly pipeline for the prediction of fusion neoantigens from tumor RNA-seq data.
icbi-lab/downloader
Easy & parallel download of FASTQ files from public repositories (SRA, EGA, GDC)
icbi-lab/current-topics-bioinformatics-lecture
icbi-lab/atlas_protocol
A computational protocol for atlas-level data integration and analysis as performed in Salcher et al. (2022).
icbi-lab/nf-deseq2
A RNA-seq differential expression analysis pipeline downstream of nf-core/rnaseq.
icbi-lab/meRanTK
methylated RNA Tool Kit
icbi-lab/nmp-liver
Single cell analysis of donor livers pre- and post machine perfusion
icbi-lab/deseq2icbi
R script to perform DE and Pathway enrichment analysis based on the output of nf-core/rnaseq
icbi-lab/DoseRider
DoseRider: Generalized Additive Mixed Models (GAMMs) for Analyzing Dose-Response Relationships in Gene Expression Data
icbi-lab/abdulrahman2021_paper
single-cell analysis for the Abdulrahman et al. (2021) paper.
icbi-lab/borst2021
single-cell analysis for the Borst et al. (2021) paper.
icbi-lab/duurland2021_paper
Single-cell analysis for Duurland et al.
icbi-lab/kortekaas2020_paper
Single cell RNA-seq analysis accompanying Kortekaas, Santegoets et al. (2020)
icbi-lab/miopy
icbi-lab/OvRSeq
OvRSeq is an R package for analyzing RNA sequencing data from ovarian cancer patients.
icbi-lab/plattner_2023
Code to reproduce figures from Plattner et al. (2022)
icbi-lab/bioconda-recipes
Conda recipes for the bioconda channel.
icbi-lab/cellxgene-user-guide
Step-by-step instructions how to use the cell-x-gene portal
icbi-lab/hairy_cell_leukemia
Single-cell analysis of Hairy Cell Leukemia samples published in Bohn et al.
icbi-lab/hgsoc
Code Repository for 'Integrated immunogenomic analyses of high-grade serous ovarian cancer reveal vulnerability to combination immunotherapy'
icbi-lab/icbi-lab.github.io
For now, redirect to ICBI website.
icbi-lab/indelicato_2023
icbi-lab/kirchmair_2023
icbi-lab/loncova_mcb_2024
Code to for the MCB chapter in "Immuno-oncology and immunotherapy" (Loncova et al. 2024)
icbi-lab/mio
icbi-lab/plattner_mcb_2024
Code for the MCB chapter in "Immuno-oncology and immunotherapy" (Plattner et al. 2024)