Nextflow Modules
Showing module(s) with keyword "proteomics"
| Module | Keywords | Description |
|---|---|---|
| nf-core/comet | spectrum identification search engine proteomics fasta mzml | Comet is an open source tandem mass spectrometry (MS/MS) sequence database search tool |
| nf-core/diamond/cluster | clustering alignment genomics proteomics | calculate clusters of highly similar sequences |
| nf-core/diamond/deepclust | clustering protein diamond deepclust proteomics | Fast graph-based protein sequence clustering using DIAMOND deepclust |
| nf-core/diamond/linclust | clustering protein diamond linclust proteomics | Fast protein sequence clustering using a greedy incremental approach |
| nf-core/diann | proteomics mass spectrometry DIA spectral library quantification | Generic DIA-NN module for running any DIA-NN operation including in-silico library generation, preliminary analysis, empirical library assembly, individual analysis, and final quantification |
| nf-core/diann/insilicolibrarygeneration | diann spectral library proteomics deep learning dia | Generate in silico predicted spectral library using DIA-NN deep learning predictor. This module uses DIA-NN software for data-independent acquisition (DIA) proteomics data processing. Output materials should include attribution: "Generated using DIA-NN". |
| nf-core/maxquant/lfq | sort proteomics mass-spectroscopy | Run standard proteomics data analysis with MaxQuant, mostly dedicated to label-free. Paths to fasta and raw files needs to be marked by "PLACEHOLDER" |
| nf-core/openms/decoydatabase | decoy database openms proteomics fasta | Create a decoy peptide database from a standard FASTA database. |
| nf-core/openms/filefilter | filter mzML openms proteomics | Filters peptide/protein identification results by different criteria. |
| nf-core/openms/idfilter | filter idXML openms proteomics | Filters peptide/protein identification results by different criteria. |
| nf-core/openms/idmassaccuracy | mass_error openms proteomics | Calculates a distribution of the mass error from given mass spectra and IDs. |
| nf-core/openms/idmerger | merge idXML openms proteomics | Merges several idXML files into one idXML file. |
| nf-core/openms/idripper | split idXML openms proteomics | Split a merged identification file into their originating identification files |
| nf-core/openms/idscoreswitcher | switch score idXML openms proteomics | Switches between different scores of peptide or protein hits in identification data |
| nf-core/openms/peakpickerhires | peak picking mzml openms proteomics | A tool for peak detection in high-resolution profile data (Orbitrap or FTICR) |
| nf-core/openms/peptideindexer | refresh idXML openms proteomics | Refreshes the protein references for all peptide hits. |
| nf-core/openms/psmfeatureextractor | features idXML openms percolator proteomics psm | Computes extra features for each input PSM for use with Percolator rescoring. |
| nf-core/openms/textexporter | export openms proteomics text tsv | Exports various OpenMS XML formats (featureXML, consensusXML, idXML, mzML) to a human-readable text format. |
| nf-core/openmsthirdparty/cometadapter | search engine fasta mzml openms proteomics | Annotates MS/MS spectra using Comet. |
| nf-core/proteus/readproteingroups | proteomics |