Repositories list

• MetaMorpheus

  Public
  Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities

  discoverycalibrationproteome+ 6spectraptmdatabase-searchuniprotmass-matchproteomics-database-search

  C#

  •

  MIT License

  •46•91•202•39•Updated Nov 22, 2024Nov 22, 2024

• FlashLFQ

  Public
  Ultra-fast label-free quantification algorithm for mass-spectrometry proteomics

  chemistryproteomicsmass-spectrometry+ 1quantification

  C#

  •

  GNU Lesser General Public License v3.0

  •14•19•31•4•Updated Nov 22, 2024Nov 22, 2024

• mzLib

  Public
  Library for mass spectrometry projects

  chemistrymass-spectrometrychemical-formulas+ 5isotopesproteomics-dataspectra-filesproteogenomicsmass-spectrometry-data

  C#

  •

  GNU Lesser General Public License v3.0

  •33•26•54•27•Updated Nov 19, 2024Nov 19, 2024

• Jenkins-MetaMorpheus

  Public
  Code used for continuous builds of MetaMorpheus

  C#

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Sep 13, 2024Sep 13, 2024

• Spritz

  Public
  Software for RNA-Seq analysis to create sample-specific proteoform databases from RNA-Seq data

  snakemakeproteomicsproteogenomics+ 3snakemake-pipelinebioinformaticsrna-seq

  C#

  •

  MIT License

  •11•7•25•0•Updated Jun 19, 2024Jun 19, 2024

• MetaPAL

  Public
  A framework for reading and writing ML-ready proteomics data

  C#

  •

  Apache License 2.0

  •7•0•3•4•Updated Apr 15, 2024Apr 15, 2024

• ProteaseGuru

  Public
  C#

  •

  GNU General Public License v3.0

  •5•3•8•1•Updated Nov 7, 2023Nov 7, 2023

• ProteoformSuite

  Public
  Construction, quantification, and visualization of proteoform families

  ptmproteoformvisualization+ 4cytoscapequantificationproteomeproteoform-families

  C#

  •

  GNU General Public License v3.0

  •19•12•23•1•Updated Jun 16, 2023Jun 16, 2023

• MetaNetwork

  Public
  HTML

  •5•9•6•1•Updated Jan 14, 2023Jan 14, 2023

• SnpEff

  Public
  This is a customized version of SnpEff used in Spritz (https://github.com/smith-chem-wisc/Spritz), which outputs a protein FASTA and XML files that can be used in MS proteomic search software.

  Java

  •81•2•0•0•Updated Jan 12, 2023Jan 12, 2023

• RawFileReader

  Public
  C#

  •20•0•0•0•Updated Jul 12, 2022Jul 12, 2022

• mzLib-rest

  Public
  Library for mass spectrometry projects

  C#

  •

  GNU Lesser General Public License v3.0

  •33•0•0•0•Updated Jul 7, 2022Jul 7, 2022

• AppleTurnover

  Public
  Application for Elucidating Turnover Rates

  C#

  •

  MIT License

  •4•0•0•0•Updated Feb 15, 2022Feb 15, 2022

• LncRNA-Snakemake

  Public
  The full LncRNA data analysis workflow from sample.fastq to IsoMat.txt

  Python

  •0•0•0•0•Updated Dec 16, 2021Dec 16, 2021

• ProteoformExplorer

  Public
  Proteoform Dashboard

  C#

  •

  MIT License

  •3•0•13•0•Updated Nov 1, 2021Nov 1, 2021

• ProteoformClassifier

  Public
  Classifies proteoform identifications and validates that input is transparent about ambiguity

  C#

  •

  MIT License

  •1•1•1•0•Updated Aug 10, 2021Aug 10, 2021

• psi-mod-CV

  Public
  Reactivated PSI-MOD ontology for molecular mass modifications

  13•0•0•0•Updated Dec 8, 2020Dec 8, 2020

• MetaDrive

  Public
  C#

  •2•0•0•0•Updated Sep 9, 2020Sep 9, 2020

• Learning-CSharp

  Public
  A Course for Learning the C# Programming Language

  MIT License

  •0•0•0•0•Updated May 11, 2020May 11, 2020

• HackyButFunctionalCodeToMakeLifeEasier

  Public
  The name says it all. Made public by Lei's request. Use at your own risk.

  C#

  •0•0•0•0•Updated Aug 29, 2019Aug 29, 2019

• ProteoformSuiteVignettes

  Public
  Vignettes for Proteoform Suite

  2•0•0•0•Updated May 16, 2019May 16, 2019

• Proteogenomics

  Public
  C# implementation of classes and functions for proteogenomics

  C#

  •2•1•2•0•Updated Mar 30, 2019Mar 30, 2019

• ThermoRawFileParser

  Public
  Thermo RAW file parser that runs on Linux with mono

  C#

  •

  Other

  •50•0•0•0•Updated Oct 22, 2018Oct 22, 2018

• MetaMorpheus-Peptide-Database-Generator

  Public
  Creates a .fasta database from MetaMorpheus PSM results

  MIT License

  •0•0•0•0•Updated Oct 12, 2018Oct 12, 2018

• Neo

  Public
  C#

  •0•0•0•0•Updated May 18, 2018May 18, 2018

• Bio.VCF

  Public
  A CSharp Parser for VCF Files

  C#

  •7•2•0•0•Updated May 14, 2018May 14, 2018

• StefanPaper

  Public
  TeX

  •0•0•0•0•Updated Mar 18, 2018Mar 18, 2018

• DeconvolutionAutoIT

  Public
  AutoIT code for devonvoluting intervals of intact protein MS data using Protein Deconvolution 2.0 on the Smith Lab's Velos search computer

  AutoIt

  •2•0•0•0•Updated Jan 18, 2018Jan 18, 2018

• gptmd

  Public
  Use open search results (from Morpheus) to create a database with uncovered candidate PTM annotations

  Python

  •7•4•0•1•Updated Sep 12, 2017Sep 12, 2017

• PrivateNeo

  Public
  OLD. SEE https://github.com/zrolfs/MetaMorpheus/tree/Neo-Fusion for current code. Downstream analysis for MetaMorpheus to identify novel spliced peptides

  C#

  •0•0•8•0•Updated Aug 11, 2017Aug 11, 2017