pridepy — Peer-reviewed • Rank 9.7 • Science 100%

pridepy: A Python package to download and search data from PRIDE database - Published in JOSS (2025)

HistoJS — Peer-reviewed • Rank 3.1 • Science 98%

HistoJS: Web-Based Analytical Tool for Advancing Multiplexed Images - Published in JOSS (2024)

gget • Rank 20.2 • Science 67%

🧬 gget enables efficient querying of genomic reference databases

ionmob • Rank 7.8 • Science 77%

An open-source prediction framework for peptide ion collision cross section (CCS) values with python.

secat • Rank 6.8 • Science 77%

Size-Exclusion Chromatography Algorithmic Toolkit

MSnbase • Rank 21.7 • Science 59%

Base Classes and Functions for Mass Spectrometry and Proteomics

pRoloc • Rank 17.9 • Science 59%

A unifying bioinformatics framework for organelle proteomics

cosmosR • Rank 15.7 • Science 59%

COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.

NormalyzerDE • Rank 15.2 • Science 59%

Tools for normalization, evaluation of outliers, technical biases and batch effects and differential expression analysis.

https://github.com/bigbio/sdrf-pipelines • Rank 14.1 • Science 59%

`sdrf-pipelines` is the official SDRF file validator and converts SDRF to pipeline configuration files

mzcore • Rank 5.9 • Science 67%

A Rust library for peptide centric mass spec calculations centered around ProForma and complex theoretical fragmentation

proteomics-sample-metadata • Rank 9.1 • Science 59%

The Proteomics sample metadata: Standard for experimental design annotation in proteomics datasets

Spectra • Rank 18.4 • Science 49%

Low level infrastructure to handle MS spectra

pixelgen-pixelator • Rank 10.1 • Science 57%

A command-line tool and library to process and analyze sequencing data from Molecular Pixelation (MPX) and Proximity Network (PNA) assays.

https://github.com/compomics/compomics-utilities • Rank 7.0 • Science 59%

Open source Java library for computational proteomics

PTXQC • Rank 16.6 • Science 49%

A Quality Control (QC) pipeline for Proteomics (PTX) results generated by MaxQuant

scp • Rank 15.5 • Science 49%

Single cell proteomics data processing

ezaai • Rank 5.9 • Science 57%

EzAAI - High Throughput Prokaryotic AAI Calculator

deeplc • Rank 13.9 • Science 49%

DeepLC: Retention time prediction for (modified) peptides using Deep Learning.

alphapept • Rank 13.7 • Science 49%

A modular, python-based framework for mass spectrometry. Powered by nbdev.

pyprophet • Rank 12.4 • Science 49%

PyProphet: Semi-supervised learning and scoring of OpenSWATH results.

proteomicslfq • Rank 6.7 • Science 54%

Proteomics label-free quantification (LFQ) analysis pipeline

ProtGenerics • Rank 18.9 • Science 36%

S4 generic functions for Bioconductor mass spectrometry infrastructure

pypdb • Rank 17.4 • Science 36%

A Python API for the RCSB Protein Data Bank (PDB)

protti • Rank 16.0 • Science 36%

Picotti lab data analysis package.

alphastats • Rank 12.3 • Science 39%

Python Package for the downstream analysis of mass-spectrometry-based proteomics data

https://github.com/compomics/ms2rescore • Rank 12.1 • Science 39%

Modular and user-friendly platform for AI-assisted rescoring of peptide identifications

piqmie • Rank 1.8 • Science 49%

Proteomics Identifications & Quantitations Data Management & Integration Service

openms • Rank 12.6 • Science 36%

The codebase of the OpenMS project

annotator • Rank 4.5 • Science 44%

A simple tool to help you manually discover the depths of your (complex) spectra, one spectrum at a time.

protViz • Rank 10.5 • Science 36%

Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics

mspms • Rank 9.3 • Science 36%

R package for the analysis of Multiplex Substrate Profiling by Mass Spectrometry for Proteases (MSP-MS) Data

proteomics-novice-qfeatures • Rank 1.4 • Science 41%

Introduction to QFeatures, Bioconductor data object for proteomics

https://github.com/cran-task-views/omics • Rank 5.0 • Science 36%

CRAN Task View: Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

rpx • Rank 16.8 • Science 23%

R Interface to the ProteomeXchange Repository

PSMatch • Rank 3.7 • Science 36%

Peptide Spectrum Matching

https://github.com/becavin-lab/bacnet • Rank 6.0 • Science 33%

BACNET is a Java based platform to develop website for multi-omics analysis

MsQuality • Rank 12.1 • Science 26%

topdownr • Rank 14.2 • Science 23%

R-package for the analysis of Thermo Orbitrap Fusion Top-Down Proteomic Data.

https://github.com/bigbio/py-pgatk • Rank 9.7 • Science 26%

Python tools for proteogenomics analysis toolkit

https://github.com/compomics/peptide-shaker • Rank 7.7 • Science 20%

Interpretation of proteomics identification results

https://github.com/compomics/meta-proteome-analyzer • Rank 6.2 • Science 20%

MetaProteomeAnalyzer (MPA) software for analyzing and visualizing MS-based metaproteomics data.

https://github.com/a-r-j/tb-resources • Rank 0.0 • Science 26%

List of online databases and resources for Mycobacterium Tuberculosis

omicsintegrator • Rank 9.0 • Science 10%

Prize-Collecting Steiner Forests for Interactomes

https://github.com/bzhanglab/pepquery • Rank 1.9 • Science 13%

PepQuery: a targeted peptide search engine

https://github.com/compomics/mascotdatfile • Rank 4.0 • Science 10%

Java API for MS/MS search results by Mascot (Matrix Science).

dashboard • Science 49%

MOMSI Standard Landscape Review Curation Workflow & Multi-Omics Dashboard

https://github.com/compomics/searchgui • Science 36%

Highly adaptable common interface for proteomics search and de novo engines

proteogendb • Science 54%

ProteoGenDB: A Fast Proteogenomic Pipeline for Identifying Sequence Variants in Proteomics Data

https://github.com/bigbio/pgatk-io • Science 13%

High performance io library for proteogenomics

msannika • Science 39%

MS Annika is a crosslink search engine based on MS Amanda, aimed at identifying crosslinks of cleavable and non-cleavable crosslinkers from MS2 and MS3 spectra.

msamanda • Science 39%

MS Amanda is a scoring system to identify peptides out of tandem mass spectrometry data using a database of known proteins.

vivid-volcano • Science 98%

A shiny app for custom analyzes of preprocessed omics data

substrateminer: A Python package to investigate protein substrate repertoires • Science 93%

substrateminer: A Python package to investigate protein substrate repertoires - Published in JOSS (2025)

https://github.com/bzhanglab/autort • Science 23%

AutoRT: Peptide retention time prediction using deep learning

https://github.com/compomics/xtandem-parser • Science 10%

Java-based parser for X!Tandem output xml files

https://github.com/compomics/spectrum_similarity • Science 23%

Scoring functions to compare MS/MS spectra

https://github.com/compomics/moff • Science 10%

A modest Feature Finder (moFF) to extract MS1 intensities from Thermo raw file

https://github.com/compomics/fragmentation-analyzer • Science 10%

A standalone java tool for analyzing ms/ms fragmentation data.

proteinfamilies • Science 57%

Generation and update of protein families

https://github.com/cmkobel/mspipeline1 • Science 13%

🪆🦖 A snakemake wrapper around Nesvilab's FragPipe-CLI. In a perfect world, this pipeline was based on Sage.

ibaqpy • Science 67%

Absolute quantification package based on quantms.io

plf • Science 49%

Peptide location fingerprinting (PLF) is a technique capable of identifying modified proteins and potential causal mechanisms in complex biological samples. Protein Locational Fingerprinter determines statisticaly significant peptide yields from protein functional domains.

bachelor_thesis • Science 44%

Bachelor Thesis

https://github.com/bmascat/lfq-proteomics-pipeline • Science 26%

All code, bash scrypts and pipelines used to analyse and visualise proteomic data from my experiments with my first Crispr KO model.

https://github.com/bigbio/quantms-utils • Science 39%

A python library with scripts and helpers classes for quantms workflow

https://github.com/bigbio/msgfplus • Science 23%

MS-GF+ (aka MSGF+ or MSGFPlus) performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database.

reportho • Science 57%

nf-core pipeline for comparative analysis of ortholog predictions

candidatevectorsearch • Science 39%

Searching for peptide candidates using sparse matrix + matrix/vector multiplication.

ms2pip • Science 57%

MS²PIP: Fast and accurate peptide spectrum prediction for multiple fragmentation methods, instruments, and labeling techniques.

training-material • Science 26%

A collection of Galaxy-related training material

PRONE • Science 26%

R Package for preprocessing, normalizing, and analyzing proteomics data

https://github.com/bzhanglab/deeprescore • Science 13%

DeepRescore: rescore PSMs leveraging deep learning-derived peptide features

metaboverse • Science 49%

Visualization and analysis platform for metabolic data and network pattern recognition

mzrecal • Science 44%

Recalibrate Mass Spectrometry data in mzML format

https://github.com/bmascat/rna-seq-proteomics-pipeline • Science 26%

Multi-omics analysis of LFQ proteomics and transcriptomics of an ALMS1 gene knockout cell model after TGF-B pathway stimulation.

https://github.com/broadinstitute/protigy • Science 10%

Proteomics Toolset for Integrative Data Analysis

https://github.com/compomics/psm_utils • Science 39%

Common utilities for parsing and handling peptide-spectrum matches and search engine results in Python

https://github.com/compomics/thermo-msf-parser • Science 23%

Parser and viewer for thermo msf files.

https://github.com/compomics/omssa-parser • Science 10%

Java based parser for OMSSA OMX files

https://github.com/compomics/im2deep • Science 49%

Collisional cross-section prediction for modified and multiconformational peptides

https://github.com/compomics/denovogui • Science 10%

Graphical user interface for de novo sequencing of tandem mass spectra

standard-methods-apis-omics • Science 57%

Online repository for the wikiCOLOSS BEEBOOK IV

https://github.com/czbiohub-sf/protdata • Science 26%

Dataloader for common proteomics search engine outputs into AnnData format

koina • Science 26%

Democratizing ML in proteomics

dynatmt • Science 49%

Browser-tool to analyze combined SILAC/TMT data, such as mePROD or Hyperplexing

https://github.com/fgcz/specl • Science 26%

prepare peptide spectrum matches for use in targeted proteomics using R and Bioconductor

nf-encyclopedia • Science 31%

A NextFlow pipeline for chromatogram library DIA proteomics workflows

ptmvision • Science 57%

Web application for the interactive visualization and exploration of post-translational modifications of proteins from open and closed search software.

pgdb • Science 41%

ProteomeGenomics Database Creation - Nextflow Pipeline

orthology_map • Science 44%

orthology_map is a pipeline designed to integrate suite of orthology assignment tools to contribute in a consensus based scoring algorithm

https://github.com/bigbio/sdrf-cellline-metadata-db • Science 36%

SDRF Cell Line Metadata Database

https://github.com/bigbio/pgt-pangenome • Science 36%

Protegenomics analysis based on Pangenome references

proteomics-data-analysis-tutorial • Science 44%

A comprehensive tutorial for proteomics data analysis in R that utilizes packages developed by researchers at PNNL and from Bioconductor.

quantms • Science 67%

Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.

https://github.com/compomics/xilmass • Science 23%

An algorithm to identify cross-linked peptides

msannika_csm_annotation • Science 65%

Calculates Intensities of Cross-linked Peptides from MS Annika CSMs.

spatialproteomics • Science 65%

Cell segmentation and downstream analysis pipeline for spatial proteomics (MIBI & COMET).