Repositories list

• CoPheeMap

  Public
  Co-regulation map of phosphosites

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Dec 24, 2024Dec 24, 2024

• funmap

  Public
  generate gene co-function networks using omics data

  Python

  •

  MIT License

  •2•5•1•1•Updated Dec 17, 2024Dec 17, 2024

• nf-docker

  Public
  docker files for pipeline steps

  docker

  R

  •0•0•0•0•Updated Dec 16, 2024Dec 16, 2024

• WebGestaltR

  Public
  R package for WebGestalt

  R

  •13•34•16•1•Updated Nov 21, 2024Nov 21, 2024

• neoflow

  Public
  NeoFlow: a proteogenomics pipeline for neoantigen discovery

  proteogenomicsnextflow-pipelineneoantigen-prediction+ 2novel-peptide-identificationsneoantigen-discovery

  Nextflow

  •12•22•9•0•Updated Nov 16, 2024Nov 16, 2024

• sumer

  Public
  SUmmarizing Multiple Enrichment analysis Results

  R

  •4•8•0•0•Updated Nov 14, 2024Nov 14, 2024

• DeepVEP

  Public
  Python

  •0•1•0•0•Updated Sep 12, 2024Sep 12, 2024

• webgestaltpy

  Public
  Python package for WebGestalt

  Rust

  •

  GNU General Public License v3.0

  •0•1•1•0•Updated Aug 16, 2024Aug 16, 2024

• AutoRT

  Public
  AutoRT: Peptide retention time prediction using deep learning

  proteomicslc-msmspeptide-retention-time+ 1deep-learning

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •7•26•1•0•Updated Jul 31, 2024Jul 31, 2024

• neoflow2

  Public
  Nextflow

  •0•0•0•0•Updated Jul 22, 2024Jul 22, 2024

• clinicalomicsdbR

  Public
  R package for interfacing with ClinicalOmicsDB

  R

  •

  Other

  •0•4•0•0•Updated Jun 26, 2024Jun 26, 2024

• webgestalt_rust

  Public
  Rust implementation of WebGestalt

  Rust

  •

  Apache License 2.0

  •0•2•1•0•Updated Jun 20, 2024Jun 20, 2024

• funmap_aml

  Public
  HTML

  •0•0•0•0•Updated May 21, 2024May 21, 2024

• DeepRescore

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

  machine-learningdeep-learningproteomics+ 2peptide-identificationmsms

  Nextflow

  •3•6•4•0•Updated May 10, 2024May 10, 2024

• deep_learning_in_proteomics

  Public
  A list of tools on proteomics using deep learning

  23•89•0•0•Updated May 5, 2024May 5, 2024

• PepQuery

  Public
  PepQuery: a targeted peptide search engine

  proteomicsmass-spectrometrypeptide-identification+ 1proteogenomics

  Java

  •

  GNU General Public License v3.0

  •0•9•15•0•Updated May 1, 2024May 1, 2024

• NetSAM

  Public
  Network Seriation And Modularization R package

  R

  •3•3•0•0•Updated Apr 2, 2024Apr 2, 2024

• COSMO

  Public
  COSMO: COrrection of Sample Mislabeling by Omics

  R

  •5•9•4•0•Updated Mar 19, 2024Mar 19, 2024

• TAAPrediction

  Public
  R

  •0•0•0•0•Updated Mar 4, 2024Mar 4, 2024

• bzhanglab.github.io

  Public
  Zhang Lab

  HTML

  •0•0•0•0•Updated Feb 20, 2024Feb 20, 2024

• funmap_visualization

  Public
  HTML

  •0•0•0•0•Updated Feb 15, 2024Feb 15, 2024

• DeepRescore2

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

  deep-learningphosphoproteomics

  Python

  •0•2•0•0•Updated Nov 2, 2023Nov 2, 2023

• SEPepQuant

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

  R

  •

  Apache License 2.0

  •1•3•2•0•Updated Jul 26, 2023Jul 26, 2023

• py-pgatk

  Public
  Python tools for proteogenomics analysis toolkit

  Python

  •

  Apache License 2.0

  •11•0•0•0•Updated Jun 21, 2023Jun 21, 2023

• OmicsEV

  Public
  A tool for large scale omics datasets evaluation

  R

  •4•24•0•0•Updated Jun 14, 2023Jun 14, 2023

• LinkedOmicsKB_manuscript

  Public
  Core scripts for calculating associations

  0•0•0•0•Updated Jun 10, 2023Jun 10, 2023

• proms

  Public
  protein markers selection

  Python

  •

  MIT License

  •5•7•0•0•Updated Apr 4, 2023Apr 4, 2023

• GENCODE_V42_reference

  Public
  Reference preparation for proteogenomics data processing and downstream analysis

  Perl

  •

  Apache License 2.0

  •0•0•0•0•Updated Dec 5, 2022Dec 5, 2022

• nf-rnaseq

  Public
  rnaseq pipeline with nextflow

  workflowrna-seqpipeline+ 1nextflow

  Nextflow

  •0•0•0•0•Updated Jul 22, 2022Jul 22, 2022

• neoflow_html_reporter

  Public
  HTML

  •0•0•0•0•Updated May 2, 2022May 2, 2022