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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 predictionluca
Single-cell Lung Cancer Atlas with 1.2M cellsimmune_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/btz363IHCount
IHC-image analysis workflowquanTIseq
a computational pipeline for the quantification of the Tumor Immune contexture from human RNA-seq dataNeoFuse
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 Kitsmartseq2_pipeline
A pipeline for processing single cell RNA-seq data generated with the SmartSeq2 protocol -- Now on nf-core: https://github.com/nf-core/smartseq2nmp-liver
Single cell analysis of donor livers pre- and post machine perfusionatlas_protocol
A computational protocol for atlas-level data integration and analysis as performed in Salcher et al. (2022).deseq2icbi
R script to perform DE and Pathway enrichment analysis based on the output of nf-core/rnaseqDoseRider
DoseRider: Generalized Additive Mixed Models (GAMMs) for Analyzing Dose-Response Relationships in Gene Expression Dataduurland2021_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.Love Open Source and this site? Check out how you can help us