RNA-seq
nf-core/rnaseqMultiple aligners and quantification methods, with comprehensive QC and gene / transcript-level quantification.
Typical outputs: expression matrices, alignment statistics and quality reports.
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Take a study from data to results
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One run setup
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Data and samples together
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Connect compatible tools, or import an existing Nextflow DSL2 project from ZIP or Git. Native imports retain their source structure and are checked for runtime compatibility.
Manage a personal pipeline and its versions, then choose data and parameters in the shared run setup.
Import a Nextflow projectChIP-seq
nf-core/chipseqProcess protein-DNA interaction sequencing data through alignment, peak calling and quality assessment.
Typical outputs: peak regions, coverage files and quality reports.
Choose in the appATAC-seq
nf-core/atacseqFor chromatin accessibility studies, detecting open chromatin regions and regulatory elements.
Typical outputs: accessible chromatin regions, coverage files and quality reports.
Choose in the appSarek variant calling
nf-core/sarekGermline and somatic variant analysis for WGS / WES data, with functional annotation.
Typical outputs: variant files, annotations and quality results, depending on selected steps.
Choose in the appMethyl-seq
nf-core/methylseqWhole-genome methylation analysis for WGBS and RRBS data.
Typical outputs: methylation calls, coverage and quality reports.
Choose in the appSpatial transcriptomics
nf-core/spatialvi10x Genomics Visium spatial transcriptomics analysis with Space Ranger and downstream steps.
Typical outputs: spatial expression results and pipeline reports, depending on inputs and parameters.
Choose in the appResearch workspace
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Nextflow execution
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Data and compute
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Find an entry point from a paper
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Data, analyses and reports in one workspace
Start with your next analysis
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