Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
☆38May 6, 2024Updated last year
Alternatives and similar repositories for quantms
Users that are interested in quantms are comparing it to the libraries listed below
Sorting:
- Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Iso…☆68Mar 13, 2026Updated last week
- A library for QC report based on MultiQC framework☆29Updated this week
- qpx (Quantitative Proteomics eXchange) format (aka quantms.io) a format to capture a full proteomics experiment☆16Updated this week
- Single cell proteomics data processing☆30Feb 9, 2026Updated last month
- R-based package for detecting differentially abundant proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass …☆30Jul 28, 2025Updated 7 months ago
- The triqler (TRansparent Identification-Quantification-linked Error Rates)'s source and example code☆26Oct 2, 2025Updated 5 months ago
- A graph visualisation tool targeted at persistent homology applications.☆11Jul 28, 2020Updated 5 years ago
- `sdrf-pipelines` is the official SDRF file validator and converts SDRF to pipeline configuration files☆29Mar 13, 2026Updated last week
- Recommendations to contenarized your bioinformatics software☆12May 30, 2018Updated 7 years ago
- Implementation of the MSqRob analysis of differentially expressed proteins using the Features infrastructure☆13Dec 17, 2025Updated 3 months ago
- A Comet-based, best practices proteomics pipeline.☆39Mar 21, 2024Updated 2 years ago
- Automated quantitative analysis of DIA proteomics mass spectrometry measurements.☆21Jan 13, 2025Updated last year
- DIA-NN - a universal automated software suite for DIA proteomics data analysis.☆429Feb 5, 2026Updated last month
- Material for the 2017 May Institute☆13Jun 25, 2017Updated 8 years ago
- ☆15May 30, 2025Updated 9 months ago
- R package - MSstats☆92Mar 13, 2026Updated last week
- MS File ToolBox - tools for parsing some mass-spectrometry related file formats (mzML, mzXML, pep.xml, prot.xml, etc.)☆12Aug 26, 2022Updated 3 years ago
- PeptideProphet, PTMProphet, ProteinProphet, iProphet, Abacus, and FDR filtering☆125Feb 12, 2026Updated last month
- A pipeline to investigate horizontal gene transfer from NGS data☆26Nov 20, 2025Updated 4 months ago
- Instant Clue - Interactive Data Analysis☆21Apr 9, 2025Updated 11 months ago
- Layered enrichment analysis tool enables facile enrichment using various statistics at once.☆18Mar 11, 2026Updated last week
- Proteomics search & quantification so fast that it feels like magic☆278Mar 12, 2026Updated last week
- Proteomics label-free quantification (LFQ) analysis pipeline☆37Jan 13, 2025Updated last year
- The `multiGSEA` R package was designed to run a robust GSEA-based pathway enrichment for multiple omics layers.☆21Oct 30, 2025Updated 4 months ago
- gatk4 RNA variant calling pipeline☆59Mar 9, 2026Updated last week
- MS-DAP: downstream analysis pipeline for quantitative proteomics☆42Jan 25, 2026Updated last month
- A pipeline for droplet-based single-cell RNA-seq and spot-based spatial transcriptomics data secondary analysis implemented in the drake …☆15Aug 27, 2025Updated 6 months ago
- ☆14Aug 22, 2022Updated 3 years ago
- TQSLE v1.0 released☆10Aug 29, 2023Updated 2 years ago
- CLI to automate Nextflow pipeline testing☆12Dec 15, 2025Updated 3 months ago
- Pipeline to evaluate and validate the accuracy of variant calling methods in genomic research☆41Updated this week
- A Deep LEArning-based Mass Spectra Embedder for spectral similarity scoring☆11Jun 18, 2025Updated 9 months ago
- Estimation of isoelectric point of peptides and proteins using support vector machines (SVM).☆10Sep 10, 2016Updated 9 years ago
- ☆57Jan 2, 2024Updated 2 years ago
- Flexible Integration of single-cell RNA-sequencing data for large-scale Multi-tissue cell atlas datasets☆13Sep 20, 2022Updated 3 years ago
- Multi-modal single cell analysis pipelines☆62Dec 11, 2025Updated 3 months ago
- DART-ID: retention time alignment and peptide identification confidence updates☆18Mar 17, 2025Updated last year
- Compare the quality of multiple genomes, along with their annotations.☆20Mar 9, 2026Updated last week
- A repository of Python tips for common data science tasks, including dataset unit testing and machine learning development for production☆18Apr 10, 2022Updated 3 years ago