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website
Publicmodules
Publicops
Publiconcoanalyser
Publictest-datasets
Publictools
Publicraredisease
PublicCall and score variants from WGS/WES of rare disease patients.setup-nextflow
Publicpathogensurveillance
Publicdemultiplex
PublicDemultiplexing pipeline for sequencing datadetaxizer
PublicA pipeline to identify (and remove) certain sequences from raw genomic data. Default taxa to identify (and remove) are Homo and Homo sapiens. Removal is optional.taxprofiler
PublicHighly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic datarangeland
PublicPipeline for remotely sensed imagery. The pipeline processes satellite imagery alongside auxiliary data in multiple steps to arrive at a set of trend files related to land-cover changes.differentialabundance
Publicdemo
Publiceager
PublicA fully reproducible and state-of-the-art ancient DNA analysis pipelinemethylseq
PublicMethylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackelmag
PublicAssembly and binning of metagenomescircrna
PubliccircRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq dataconfigs
PublicConfig files used to define parameters specific to compute environments at different Institutionscrisprseq
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`).metapep
Publicscrnaseq
PublicA single-cell RNAseq pipeline for 10X genomics datascdownstream
PublicA single cell transcriptomics pipeline for QC, integration and making the data presentablefastquorum
Publictfactivity
PublicBioinformatics pipeline that makes use of expression and open chromatin data to identify differentially active transcription factors across conditions.troughgraph
Publicmethylarray
PublicProcess 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.rnafusion
Public