Repositories list

• pheno_analysis

  Public
  Jupyter Notebook

  •0•0•0•1•Updated Dec 11, 2024Dec 11, 2024

• DeepPCT

  Public
  An integrated framework to predict PTM crosstalk within proteins

  Python

  •

  GNU General Public License v3.0

  •2•0•0•0•Updated Nov 22, 2024Nov 22, 2024

• MassiveFold

  Public
  Python

  •

  Other

  •10•0•0•0•Updated Nov 9, 2024Nov 9, 2024

• rustyms

  Public
  A rust library for parsing Pro Forma peptides and matching them against MS spectra

  Rust

  •

  Apache License 2.0

  •6•0•0•0•Updated Nov 8, 2024Nov 8, 2024

• LiP-processing-script

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Nov 1, 2024Nov 1, 2024

• AI2BMD

  Public
  AI-powered ab initio biomolecular dynamics simulation

  Python

  •

  MIT License

  •51•0•0•0•Updated Oct 17, 2024Oct 17, 2024

• RoseTTAFold2-PPI

  Public
  Fast deep learning methods for large-scale protein-protein interaction screening

  Python

  •

  GNU General Public License v3.0

  •7•0•0•0•Updated Oct 2, 2024Oct 2, 2024

• ibaqpy

  Public
  Absolute quantification package based on quantms.io

  Python

  •

  MIT License

  •9•0•0•0•Updated Aug 21, 2024Aug 21, 2024

• ProteinMPNN

  Public
  Code for the ProteinMPNN paper

  Jupyter Notebook

  •

  MIT License

  •313•0•0•0•Updated Aug 14, 2024Aug 14, 2024

• GSEApy

  Public
  Gene Set Enrichment Analysis in Python

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •119•0•0•0•Updated Aug 5, 2024Aug 5, 2024

• PINNACLE

  Public
  Contextualizing protein representations using deep learning on protein networks and single-cell data

  Python

  •

  MIT License

  •18•0•0•0•Updated Jul 29, 2024Jul 29, 2024

• LINGER

  Public
  17•0•0•0•Updated Jul 29, 2024Jul 29, 2024

• PEPPI

  Public
  Pipeline for protein-protein interaction prediction

  Fortran

  •

  GNU General Public License v3.0

  •7•0•0•0•Updated Jul 24, 2024Jul 24, 2024

• pka_for_ptm

  Public
  Code for finding pKa for post translational modification sites

  Python

  •0•0•0•0•Updated Jul 23, 2024Jul 23, 2024

• pypath

  Public
  Python module for prior knowledge integration. Builds databases of signaling pathways, enzyme-substrate interactions, complexes, annotations and intercellular communication roles.

  Python

  •

  GNU General Public License v3.0

  •47•0•0•0•Updated Jul 18, 2024Jul 18, 2024

• inmoose

  Public
  InMoose is the INtegrated Multi Omic Open Source Environment. It is a collection of tools for the analysis of omic data.

  Python

  •

  GNU General Public License v3.0

  •5•0•0•0•Updated Jul 17, 2024Jul 17, 2024

• alphaflow

  Public
  AlphaFold Meets Flow Matching for Generating Protein Ensembles

  Python

  •

  MIT License

  •51•0•0•0•Updated Jun 20, 2024Jun 20, 2024

• RF2-Lite

  Public
  Python

  •5•0•0•0•Updated Jun 1, 2024Jun 1, 2024

• evoformer_representation

  Public
  Python

  •

  MIT License

  •5•0•0•0•Updated May 13, 2024May 13, 2024

• awesome-multi-omics

  Public
  List of software packages for multi-omics analysis

  MIT License

  •163•0•0•0•Updated Apr 23, 2024Apr 23, 2024

• GREMLIN_LH

  Public
  Jupyter Notebook

  •3•0•0•0•Updated Apr 22, 2024Apr 22, 2024

• MSstatsLiP

  Public
  HTML

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

• phosx

  Public
  Kinase activity inference from phosphosproteomics data

  Python

  •

  Apache License 2.0

  •1•0•0•0•Updated Mar 22, 2024Mar 22, 2024

• RSRM

  Public
  code of ICLR 2024 paper Reinforcement Symbolic Regression Machine

  Python

  •

  MIT License

  •2•0•0•0•Updated Feb 19, 2024Feb 19, 2024

• ProForma

  Public
  HUPO-PSI Standardized peptidoform notation

  4•0•0•0•Updated Feb 12, 2024Feb 12, 2024

• cell_cycle_model

  Public
  Component Pascal

  •

  MIT License

  •2•0•0•0•Updated Jan 14, 2024Jan 14, 2024

• BacterAI

  Public
  HTML

  •7•0•0•0•Updated Dec 20, 2023Dec 20, 2023

• harissa

  Public
  Tools for mechanistic gene network inference from single-cell data

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •1•0•0•0•Updated Dec 18, 2023Dec 18, 2023

• PPIprophet

  Public
  PPI prophet is a software tool for analysis of AP fractionated samples

  Python

  •

  MIT License

  •1•0•0•0•Updated Oct 24, 2023Oct 24, 2023

• BINGO

  Public
  MATLAB

  •

  MIT License

  •4•0•0•0•Updated Jan 27, 2022Jan 27, 2022