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ICBI (@icbi-lab)

icbi-lab

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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

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

IHCount

IHC-image analysis workflow

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.

current-topics-bioinformatics-lecture

downloader

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

nf-deseq2

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

meRanTK

methylated RNA Tool Kit

smartseq2_pipeline

A pipeline for processing single cell RNA-seq data generated with the SmartSeq2 protocol -- Now on nf-core: https://github.com/nf-core/smartseq2

nmp-liver

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

atlas_protocol

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

Jupyter Notebook

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

duurland2021_paper

Single-cell analysis for Duurland et al.

kortekaas2020_paper

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

borst2021

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

abdulrahman2021_paper

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

miopy

OvRSeq

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