Top 7 proteomic Open-Source Projects

training-material

1 295 10.0 HTML

A collection of Galaxy-related training material
pypdb

1 299 4.8 Python

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

www.influxdata.com featured

Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.
sage

5 198 7.7 Rust

Proteomics search & quantification so fast that it feels like magic (by lazear)

Project mention: Does anyone know a great guide/documentation explaining how to implement Percolator? | /r/proteomics | 2023-06-06

If you want to implement LDA from scratch, you could check out how Sage is doing it.

alphapept

2 160 6.4 HTML

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

1 53 6.3 R

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

1 37 3.4 Python

Fast and flexible semi-supervised learning for peptide detection in Python

Project mention: Does anyone know a great guide/documentation explaining how to implement Percolator? | /r/proteomics | 2023-06-06

Why not use MokaPot instead? It’s fundamentally a python installation of percolator. https://github.com/wfondrie/mokapot

enrich_omics

2 17 3.6 Python

A python package to explore pathways, diseases and drugs associated to a list of targets (genes, proteins, etc)
SaaSHub

www.saashub.com featured

SaaSHub - Software Alternatives and Reviews. SaaSHub helps you find the best software and product alternatives

NOTE: The open source projects on this list are ordered by number of github stars. The number of mentions indicates repo mentiontions in the last 12 Months or since we started tracking (Dec 2020).

proteomics related posts

Does anyone know a great guide/documentation explaining how to implement Percolator?

2 projects | /r/proteomics | 6 Jun 2023
What are some good examples of well-engineered bioinformatics pipelines?

8 projects | /r/bioinformatics | 5 Apr 2023
Proteomics search engine written in Rust

5 projects | /r/rust | 5 Nov 2022
Opinions on AlphaPept

2 projects | /r/proteomics | 30 Oct 2022
A python package to perform gene enrichment analysis (Bioinformatics/ health data science)

1 project | /r/coolgithubprojects | 20 Feb 2022
A note from our sponsor - SaaSHub
www.saashub.com | 29 May 2024

SaaSHub helps you find the best software and product alternatives Learn more →