pwilmart / PAW_pipelineView external linksLinks
A Comet-based, best practices proteomics pipeline.
☆39Mar 21, 2024Updated last year
Alternatives and similar repositories for PAW_pipeline
Users that are interested in PAW_pipeline are comparing it to the libraries listed below
Sorting:
- The Interactive Peptide Spectral Annotator☆21Jun 9, 2020Updated 5 years ago
- Utilities for downloading and managing protein FASTA files.☆14Mar 20, 2024Updated last year
- This project is created by the Hao Lab at the Chemistry Department in George Washington University, Washington, D.C. This project aims to…☆31Nov 24, 2024Updated last year
- R-based package for detecting differentially abundant proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass …☆29Jul 28, 2025Updated 6 months ago
- A python interface to the SAGE search engine for mass spectrometry proteomics☆15Jan 16, 2026Updated last month
- Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Iso…☆38May 6, 2024Updated last year
- MS-DAP: downstream analysis pipeline for quantitative proteomics☆40Jan 25, 2026Updated 3 weeks ago
- Post Translational Modification (PTM) Significance Analysis in shotgun mass spectrometry-based proteomic experiments☆13Updated this week
- Scalable, accurate and sensitive protein group FDRs for large-scale mass spectrometry experiments☆13May 23, 2025Updated 8 months ago
- Peptide Correlation analysis☆11Oct 3, 2024Updated last year
- Post-processing peptide de novo sequences to improve their accuracy☆10Nov 29, 2022Updated 3 years ago
- The Git Account of LCMSMethods.org☆11Jun 1, 2019Updated 6 years ago
- The triqler (TRansparent Identification-Quantification-linked Error Rates)'s source and example code☆26Oct 2, 2025Updated 4 months ago
- This is a collection of minimal code to visualize various aspects of proteomics data.☆82Jan 6, 2022Updated 4 years ago
- Interpretation of proteomics identification results☆53Nov 26, 2025Updated 2 months ago
- Navigation links (and brief descriptions) to my repositories.☆12Nov 25, 2025Updated 2 months ago
- MS-GF+ (aka MSGF+ or MSGFPlus) performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence …☆83Oct 23, 2025Updated 3 months ago
- Spectral library searching using approximate nearest neighbor techniques.☆48Updated this week
- FRAMA: From RNA-seq data to annotated mRNA assemblies☆12Sep 28, 2018Updated 7 years ago
- Implementation of the MSqRob analysis of differentially expressed proteins using the Features infrastructure☆13Dec 17, 2025Updated last month
- DIA-NN - a universal automated software suite for DIA proteomics data analysis.☆421Feb 5, 2026Updated last week
- Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Iso…☆68Jan 21, 2026Updated 3 weeks ago
- A cross-platform proteomics data analysis suite☆276Updated this week
- StatsPro : systematic integration and evaluation of statistical approaches for detecting differential expression in label-free quantitat…☆13Mar 13, 2022Updated 3 years ago
- A tool integrates channel abundances from multiple TMT samples and exports a general report for downstream analysis.☆13Feb 9, 2026Updated last week
- Brings Orbitrap mass spectrometry data to life; multi-platform, fast and colorful R package☆37May 1, 2024Updated last year
- Proteomics search & quantification so fast that it feels like magic☆270Jan 6, 2026Updated last month
- a toolbox for metabolomic data analysis, visualization and ‘omic’ integration☆13Jun 21, 2018Updated 7 years ago
- Tools for Batch Effects Diagnostics and Correction☆17Apr 25, 2025Updated 9 months ago
- ☆15Apr 27, 2022Updated 3 years ago
- Construction, quantification, and visualization of proteoform families☆14Dec 16, 2024Updated last year
- Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics☆127Jan 13, 2026Updated last month
- Examples of TMT data analyses using R. Links to notebooks and repositories. Also a few spectral counting analyses.☆22May 27, 2022Updated 3 years ago
- GEO RNA-seq Experiments Processing Pipeline☆22Oct 25, 2019Updated 6 years ago
- PeptideProphet, PTMProphet, ProteinProphet, iProphet, Abacus, and FDR filtering☆125Updated this week
- An open-source Python package for the visual annotation of proteomics data with sequence specific knowledge.☆92Nov 17, 2025Updated 2 months ago
- Fast and flexible semi-supervised learning for peptide detection in Python☆49Feb 27, 2025Updated 11 months ago
- A python package for fast post translational modification localization, powered by Cython.☆20Dec 15, 2023Updated 2 years ago
- R package - MSstats☆91Jan 29, 2026Updated 2 weeks ago