Computational Omics and Systems Biology Group

Repositories

• ThermoRawFileParser

  Thermo RAW file parser that runs on Linux with mono
  C# 21 52 10 0 Updated Jun 1, 2020

• peptide-shaker

  Interpretation of proteomics identification results

  bioinformatics proteomics protein-identification
  Java 21 23 55 (14 issues need help) 0 Updated May 29, 2020

• COSS

  COSS: CompOmics Spectral Searching
  Java 1 2 2 1 Updated May 28, 2020

• compomics.github.io

  Compomics github website.
  Python MIT 1 0 0 0 Updated May 28, 2020

• DeepLC

  DeepLC: Retention time prediction for (modified) peptides using Deep Learning.
  Python Apache-2.0 1 8 2 0 Updated May 28, 2020

• compomics-utilities

  Open source Java library for computational proteomics

  bioinformatics proteomics computational-proteomics
  Java Apache-2.0 20 19 3 (2 issues need help) 0 Updated May 28, 2020

• searchgui

  Highly adaptable common interface for proteomics search and de novo engines

  bioinformatics proteomics protein-identification
  Java 16 20 20 (12 issues need help) 0 Updated May 27, 2020

• ms2pip_c

  MS2PIP: MS2 Peak Intensity Prediction
  C Apache-2.0 8 12 4 4 Updated May 26, 2020

• ThermoRawFileParserGUI

  Graphical user interface for the ThermoRawFileParser

  java conversion proteomics raw
  Java Apache-2.0 0 6 0 0 Updated May 11, 2020

• moFF

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

  proteomics mass-spectrometry apex-intensity-ms1
  Python 11 30 3 0 Updated Apr 29, 2020

• colims

  A lims system to automate and expedite proteomics data management, processing and analysis.
  APL 0 3 0 2 Updated Apr 23, 2020

• pride-asa-pipeline

  Uniform annotation of identified spectra.
  Java Apache-2.0 2 0 1 (1 issue needs help) 1 Updated Apr 23, 2020

• mass-modifications

  A list of peptide mass modifications, mapping multiple resources, and a Python interface.
  Apache-2.0 0 0 0 0 Updated Apr 12, 2020

• secrete-site
  JavaScript 0 0 0 0 Updated Apr 2, 2020

• D012554

  Machine Leren methoden voor biomedische gegevens
  Jupyter Notebook 2 0 0 0 Updated Mar 29, 2020

• meta-proteome-analyzer

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

  bioinformatics-pipeline software proteomics metaproteomics protein-identification database-searchtool
  TSQL Apache-2.0 5 14 11 0 Updated Mar 26, 2020

• omssa-parser

  Java based parser for OMSSA OMX files

  bioinformatics proteomics omssa
  Java Apache-2.0 0 0 0 0 Updated Mar 23, 2020

• scop3d

  Sequence conservation of protein on 3D structure.
  Python GPL-3.0 3 1 0 0 Updated Mar 10, 2020

• bioconda-recipes

  Forked from bioconda/bioconda-recipes

  Conda recipes for the bioconda channel.
  Shell 1,470 0 0 0 Updated Mar 4, 2020

• MS2IO

  Library to read and write ms2 spectrum file
  Java 0 0 0 0 Updated Feb 27, 2020

• pepshell

  Visualization of conformational proteomics data.
  Java 0 0 1 1 Updated Feb 26, 2020

• mascotdatfile

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

  bioinformatics proteomics mascot
  Java Apache-2.0 0 2 0 0 Updated Feb 26, 2020

• compomics-rover

  A tool to visualize and validate quantitative proteomics data from different sources.
  Java Apache-2.0 0 0 2 0 Updated Feb 26, 2020

• denovogui

  Graphical user interface for de novo sequencing of tandem mass spectra

  proteomics denovo graphical-user-interface de-novo-sequencing
  Java 6 5 2 0 Updated Jan 31, 2020

• reporter

  Protein quantification based on reporter ions

  bioinformatics proteomics protein-quantification reporter-ions
  Java 1 2 2 (2 issues need help) 0 Updated Jan 26, 2020

• jsparklines

  Sparklines for java tables

  visualization sparkline
  Java Apache-2.0 2 6 0 0 Updated Jan 26, 2020

• cellmissy

  Cell Migration Invasion Storage System.
  Java Apache-2.0 3 4 0 0 Updated Dec 9, 2019

• ms2rescore

  Sensitive PSM rescoring with predicted MS² peak intensities using MS²PIP and Percolator.

  proteomics percolator ms2pip
  Python Apache-2.0 1 3 0 0 Updated Dec 5, 2019

• ols-dialog

  Java front end to the ontology lookup service (OLS)
  Java 1 0 0 0 Updated Nov 27, 2019

• fragmentation-analyzer

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

  bioinformatics proteomics fragmentation
  Java 1 2 3 (1 issue needs help) 0 Updated Nov 22, 2019