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Publicsetup-nextflow
Public- Process methylation data from Illumina arrays. Pre-processing, quality checks, confounder check and DMPs (differentially methylated positions) and DMRs (differentially methylated regions). Optionally estimates cell type composition and adjusts data for it.
ops
Public- Pipeline for testing drug response prediction models in a statistically and biologically sound way.
tools
Public- Longread PacBio sequencing processing for WGS and PureTarget
createtaxdb
PublicParallelised and automated construction of metagenomic classifier databases of different toolstest-datasets
Public- Demultiplexing pipeline for sequencing data
funcscan
Publicmolkart
PublicA pipeline for processing Molecular Cartography data from Resolve Bioscience (combinatorial FISH)rnavar
Publicmag
PublicAssembly and binning of metagenomesgenomeassembler
Publiceager
PublicA fully reproducible and state-of-the-art ancient DNA analysis pipelinesarek
PublicAnalysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencingdifferentialabundance
Publicsmrnaseq
Publiccrisprseq
PublicA pipeline for the analysis of CRISPR edited data. It allows the evaluation of the quality of gene editing experiments using targeted next generation sequencing (NGS) data (`targeted`) as well as the discovery of important genes from knock-out or activation CRISPR-Cas9 screens using CRISPR pooled DNA (`screening`).mhcquant
Publicmeerpipe
Publicmethylseq
PublicMethylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackelreferences
Publicnf-core/references is a bioinformatics pipeline that build references, for multiple use casesscrnaseq
PublicSingle-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detectionsetup-nf-test
Publicmagmap
Publictaxprofiler
PublicHighly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data