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pixelator
PublicPipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)variantbenchmarking
Public- Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
- Assembly and binning of metagenomes
tfactivity
PublicBioinformatics pipeline that makes use of expression and open chromatin data to identify differentially active transcription factors across conditions.- Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
oncoanalyser
Publiccreatetaxdb
PublicParallelised and automated construction of metagenomic classifier databases of different toolsmetatdenovo
PublicAssembly and annotation of metatranscriptomic or metagenomic data for prokaryotic, eukaryotic and viruses.ops
Publicwebsite
Publicpathogensurveillance
Publicsarek
PublicAnalysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencingtest-datasets
Publicmcmicro
PublicAn end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.reportho
Publicsetup-nextflow
Publicconfigs
PublicConfig files used to define parameters specific to compute environments at different Institutionsbamtofastq
PublicConverts bam or cram files to fastq format and does quality control.methylseq
PublicMethylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackeldrugresponseeval
PublicPipeline for testing drug response prediction models in a statistically and biologically sound way.- Call and score variants from WGS/WES of rare disease patients.
crisprseq
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`).drop
Publicdifferentialabundance
Publicproteinfamilies
PublicGeneration and update of protein families