Repositories list

• LinkedOmicsChat

  Public
  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 13, 2026Jun 13, 2026

• WebGestaltR

  Public
  R package for WebGestalt

  R

  •1515 forks•3838 stars•1515 issues•00 pull requests•Updated Jun 11, 2026Jun 11, 2026

• deep_learning_in_proteomics

  Public
  A list of tools on proteomics using deep learning

  2626 forks•108108 stars•00 issues•00 pull requests•Updated May 14, 2026May 14, 2026

• SEPepQuant

  Public
  SEPepQuant: a graph theory-based approach enables comprehensive protein isoform characterization in shotgun proteomics

  R

  •

  Apache License 2.0

  •22 forks•44 stars•44 issues•00 pull requests•Updated May 12, 2026May 12, 2026

• pgdia

  Public
  Nextflow code for PG-DIA

  Nextflow

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 28, 2026Apr 28, 2026

• xlranker

  Public
  prioritization tool for ppi-xl data

  bioinformaticsppiprotein-protein-interaction+ 2

  bioinformaticsppiprotein-protein-interactioncross-linkingppi-xl

  Python

  •

  MIT License

  •00 forks•11 star•11 issue•00 pull requests•Updated Apr 27, 2026Apr 27, 2026

• webgestalt_rust

  Public
  Rust implementation of WebGestalt

  Rust

  •

  Apache License 2.0

  •00 forks•55 stars•11 issue•11 pull request•Updated Apr 14, 2026Apr 14, 2026

• PepQueryMHC

  Public
  PepQueryMHC: Rapid and Comprehensive Tumor Antigen Prioritization from Immunopeptidomics Data

  proteogenomicsimmunopeptidomics

  proteogenomicsimmunopeptidomics

  Java

  •

  GNU General Public License v3.0

  •11 fork•44 stars•22 issues•00 pull requests•Updated Feb 12, 2026Feb 12, 2026

• funmap

  Public
  generate gene co-function networks using omics data

  Python

  •

  MIT License

  •44 forks•88 stars•33 issues•11 pull request•Updated Feb 4, 2026Feb 4, 2026

• metasage

  Public
  feature importance to identify interesting analytes

  Python

  •00 forks•11 star•00 issues•00 pull requests•Updated Jan 8, 2026Jan 8, 2026

• webgestaltpy

  Public
  Python package for WebGestalt

  Rust

  •

  GNU General Public License v3.0

  •00 forks•44 stars•11 issue•00 pull requests•Updated Nov 26, 2025Nov 26, 2025

• DeepMVP

  Public
  Python

  •

  GNU General Public License v3.0

  •33 forks•2828 stars•33 issues•11 pull request•Updated Oct 3, 2025Oct 3, 2025

• nf-docker

  Public
  docker files for pipeline steps

  docker

  docker

  R

  •11 fork•00 stars•00 issues•00 pull requests•Updated Aug 2, 2025Aug 2, 2025

• customprodbj

  Public
  Java

  •

  GNU General Public License v3.0

  •55 forks•33 stars•00 issues•11 pull request•Updated Jul 12, 2025Jul 12, 2025

• webgestalt_tutorial

  Public
  Tutorial of how to start from abundance data to using WebGestalt for Enrichment Analysis

  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 28, 2025Mar 28, 2025

• CoPheeMap

  Public
  Co-regulation map of phosphosites

  Jupyter Notebook

  •

  MIT License

  •11 fork•11 star•00 issues•00 pull requests•Updated Feb 28, 2025Feb 28, 2025

• neoflow

  Public
  NeoFlow: a proteogenomics pipeline for neoantigen discovery

  proteogenomicsnextflow-pipelineneoantigen-prediction+ 2

  proteogenomicsnextflow-pipelineneoantigen-predictionnovel-peptide-identificationsneoantigen-discovery

  Nextflow

  •1212 forks•2929 stars•99 issues•00 pull requests•Updated Nov 16, 2024Nov 16, 2024

• sumer

  Public
  SUmmarizing Multiple Enrichment analysis Results

  R

  •44 forks•1010 stars•00 issues•00 pull requests•Updated Nov 14, 2024Nov 14, 2024

• AutoRT

  Public
  AutoRT: Peptide retention time prediction using deep learning

  deep-learningproteomicslc-msms+ 1

  deep-learningproteomicslc-msmspeptide-retention-time

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •99 forks•3030 stars•11 issue•00 pull requests•Updated Jul 31, 2024Jul 31, 2024

• neoflow2

  Public
  Nextflow

  •00 forks•00 stars•22 issues•00 pull requests•Updated Jul 22, 2024Jul 22, 2024

• clinicalomicsdbR

  Public
  R package for interfacing with ClinicalOmicsDB

  R

  •

  Other

  •00 forks•44 stars•00 issues•00 pull requests•Updated Jun 26, 2024Jun 26, 2024

• funmap_aml

  Public
  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 21, 2024May 21, 2024

• DeepRescore

  Public
  DeepRescore: rescore PSMs leveraging deep learning-derived peptide features

  machine-learningdeep-learningproteomics+ 2

  machine-learningdeep-learningproteomicspeptide-identificationmsms

  Nextflow

  •33 forks•77 stars•44 issues•00 pull requests•Updated May 10, 2024May 10, 2024

• PepQuery

  Public
  PepQuery: a targeted peptide search engine

  proteomicsmass-spectrometrypeptide-identification+ 1

  proteomicsmass-spectrometrypeptide-identificationproteogenomics

  Java

  •

  GNU General Public License v3.0

  •22 forks•1515 stars•2727 issues•00 pull requests•Updated May 1, 2024May 1, 2024

• NetSAM

  Public
  Network Seriation And Modularization R package

  R

  •33 forks•33 stars•00 issues•00 pull requests•Updated Apr 2, 2024Apr 2, 2024

• COSMO

  Public
  COSMO: COrrection of Sample Mislabeling by Omics

  R

  •44 forks•99 stars•44 issues•00 pull requests•Updated Mar 19, 2024Mar 19, 2024

• TAAPrediction

  Public
  R

  •00 forks•11 star•00 issues•00 pull requests•Updated Mar 4, 2024Mar 4, 2024

• bzhanglab.github.io

  Public
  Zhang Lab

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 20, 2024Feb 20, 2024

• funmap_visualization

  Public
  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 15, 2024Feb 15, 2024

• DeepRescore2

  Public
  DeepRescore2: deep learning prediction boosts phosphoproteomics-based discoveries through improved phosphopeptide identification

  deep-learningphosphoproteomics

  deep-learningphosphoproteomics

  Python

  •00 forks•11 star•00 issues•00 pull requests•Updated Nov 2, 2023Nov 2, 2023