Nextflow Modules
Showing module(s) with keyword "proteomics"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/comet | Process | 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 | Process | clustering alignment genomics proteomics | calculate clusters of highly similar sequences |
| nf-core/diamond/deepclust | Process | clustering protein diamond deepclust proteomics | Fast graph-based protein sequence clustering using DIAMOND deepclust |
| nf-core/diamond/linclust | Process | clustering protein diamond linclust proteomics | Fast protein sequence clustering using a greedy incremental approach |
| nf-core/diann | Process | 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 | Process | 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/dia_proteomics_analysis | Workflow | diann proteomics dia quantification spectral library quantms-utils | Complete DIA-NN proteomics analysis pipeline including in-silico library generation, preliminary analysis, empirical library assembly, individual analysis, and final quantification. This subworkflow combines DIA-NN modules with quantms-utils for comprehensive data-independent acquisition (DIA) proteomics data processing. |
| nf-core/easypqp/convert | Process | proteomics spectral library dia pepxml idxml mzml | Convert peptide identifications (pepXML or idXML) and the matching spectra (mzML, mzXML or MGF) into EasyPQP PSM and peak pickle files for spectral library generation. |
| nf-core/easypqp/library | Process | proteomics spectral library dia openswath diann | Generate a spectral library (TSV) from EasyPQP PSM and peak pickle files. |
| nf-core/maxquant/lfq | Process | 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 | Process | decoy database openms proteomics fasta | Create a decoy peptide database from a standard FASTA database. |
| nf-core/openms/featurefinderidentification | Process | quantification feature detection featureXML openms proteomics | Detects and quantifies features in MS1 data based on peptide identifications (targeted feature extraction). |
| nf-core/openms/fileconverter | Process | file conversion mass spectrometry mzml mzxml openms proteomics | Converts between different mass spectrometry file formats (e.g. mzML, mzXML, mgf, mzData, dta, dta2d, featureXML, consensusXML, idXML). |
| nf-core/openms/filefilter | Process | filter mzML openms proteomics | Filters peptide/protein identification results by different criteria. |
| nf-core/openms/idconflictresolver | Process | quantification consensusXML openms proteomics | Resolves ambiguous annotations of features with peptide identifications, keeping the best-scoring hit per feature. |
| nf-core/openms/idfilter | Process | filter idXML openms proteomics | Filters peptide/protein identification results by different criteria. |
| nf-core/openms/idmassaccuracy | Process | mass_error |