icbi-lab Goto Github PK

abdulrahman2021_paper

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

atlas_protocol

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

bioconda-recipes

Conda recipes for the bioconda channel.

borst2021

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

cellprofiler

An open-source application for biological image analysis

cellxgene-user-guide

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

current-topics-bioinformatics-lecture

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

downloader

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

duurland2021_paper

Single-cell analysis for Duurland et al.

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.

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

indelicato_2023

infercnvpy

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

kircaller

Python tool for KIR3DS1/L1 genotyping

kirchmair_2023

kortekaas2020_paper

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

loncova_mcb_2024

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

luca

Single-cell Lung Cancer Atlas with 1.2M cells

merantk

methylated RNA Tool Kit

mio

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

nf-deseq2

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