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rnavar
Publicmodules
Publictaxprofiler
PublicHighly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data- Demultiplexing pipeline for sequencing data
meerpipe
Public- circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data
- A pipeline for processing Molecular Cartography data from Resolve Bioscience (combinatorial FISH)
- Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection
- Config files used to define parameters specific to compute environments at different Institutions
- Stochastic Testing and Input Manipulation for Unbiased Learning Systems
- Pipeline for Sequential Analysis of MacroMolecules accessibilitY sequencing (SAMMY-seq) data, to analyze chromatin state.
- Assembly and binning of metagenomes
variantbenchmarking
Publicscnanoseq
PublicSingle-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomicsfuncscan
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`).genomeassembler
Publictfactivity
PublicBioinformatics pipeline that makes use of expression and open chromatin data to identify differentially active transcription factors across conditions.proteinfamilies
PublicGeneration and update of protein familiessetup-nextflow
Publictest-datasets
Publicstats
Publicops
Publicsarek
PublicAnalysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencingpathogensurveillance
Publicphaseimpute
PublicA bioinformatics pipeline to phase and impute genetic datascdownstream
PublicA single cell transcriptomics pipeline for QC, integration and making the data presentable