Repositories list

• PSI-Interface

  Public
  C# reader/writer for mzIdentML files (.mzID). Also supports reading mzML files.

  mass-spectrometrymzmlmzidentml+ 1mzml-files

  C#

  •3•4•0•0•Updated Feb 8, 2025Feb 8, 2025

• MzidMerger

  Public
  Merges split-FASTA MS-GF+ search result .mzid files.

  mass-spectrometrymzidentmlmzid

  C#

  •0•3•0•0•Updated Feb 8, 2025Feb 8, 2025

• DataPackage-Archive-Manager

  Public
  DataPackage Archive Manager

  C#

  •0•0•0•0•Updated Feb 7, 2025Feb 7, 2025

• DMS-Organism-Database-Handler

  Public
  Organism Database (FASTA file) programs, including PRISMSeq Uploader and the FastaFileMaker console application

  C#

  •1•0•0•0•Updated Feb 6, 2025Feb 6, 2025

• DBSchema_PgSQL_DMS

  Public
  PRISM Data Management System PostgreSQL database schema

  PLpgSQL

  •0•3•0•0•Updated Feb 6, 2025Feb 6, 2025

• DMS-Website

  Public
  DMS Website

  PHP

  •0•1•0•1•Updated Jan 31, 2025Jan 31, 2025

• PNNL-PreProcessor

  Public
  Distribution binaries for the PNNL PreProcessor

  0•2•0•0•Updated Jan 31, 2025Jan 31, 2025

• PNNL.DMS.utils

  Public
  Tools to interface with PNNL's DMS in R

  dmspnnl

  R

  •0•1•5•2•Updated Jan 29, 2025Jan 29, 2025

• DMS-Analysis-Manager

  Public
  DMS Analysis Tool Manager

  C#

  •

  BSD 2-Clause "Simplified" License

  •0•3•0•0•Updated Jan 28, 2025Jan 28, 2025

• DB-Schema-Export-Tool

  Public
  Exports SQL Server and Postgres database objects as schema files. Exported objects include tables, views, stored procedures, and functions, plus also database properties including database roles and logins. The program can also export table data to create SQL files with an Insert Into statement for each row.

  sql-server-databasepostgresql-databasesql-server+ 1postgresql

  C#

  •

  BSD 2-Clause "Simplified" License

  •8•12•0•0•Updated Jan 24, 2025Jan 24, 2025

• DMS-Model-Config-Db-Updater

  Public
  Updates column names in the SQLite files used by the DMS website to retrieve data from the DMS database and display it for users

  C#

  •0•0•0•0•Updated Jan 24, 2025Jan 24, 2025

• PgSQL-Procedure-List-Updater

  Public
  Processes a PostgreSQL DDL file with procedure or function creation statements and updates each procedure or function found using a file created by the DB Schema Export Tool

  C#

  •0•0•0•0•Updated Jan 24, 2025Jan 24, 2025

• SQLServer-Stored-Procedure-Converter

  Public
  Converts SQL Server stored procedures to PostgreSQL compatible stored procedures

  PLpgSQL

  •1•4•0•0•Updated Jan 24, 2025Jan 24, 2025

• PgSQL-View-Creator-Helper

  Public
  Uses a map file to update table and column names in a SQL DDL file with Create View statements

  C#

  •0•0•0•0•Updated Jan 24, 2025Jan 24, 2025

• PgSQL-Table-Creator-Helper

  Public
  Uses a map file to update column names in a SQL DDL file with Create Index statements

  PLpgSQL

  •0•0•0•0•Updated Jan 24, 2025Jan 24, 2025

• Data-Import-Manager

  Public
  DataImportManager (DIM)

  C#

  •0•0•0•0•Updated Jan 23, 2025Jan 23, 2025

• PlexedPiper

  Public
  proteomicsisobaric-labeling

  R

  •7•2•1•2•Updated Jan 22, 2025Jan 22, 2025

• MSnSet.utils

  Public
  custom wrappers of frequently used R code

  R

  •8•6•5•1•Updated Jan 21, 2025Jan 21, 2025

• TopPICR

  Public
  R package for processing results from TopPIC, including resolving ambiguity in proteoform identification

  R

  •

  GNU General Public License v3.0

  •2•4•0•0•Updated Jan 21, 2025Jan 21, 2025

• AmpsSDK

  Public
  SDK for controlling the Adaptable Multiple Power Supplies (AMPS boxes)

  C#

  •

  MIT License

  •3•2•0•0•Updated Jan 18, 2025Jan 18, 2025

• DMS-Capture-Task-Manager

  Public
  DMS Capture Task Manager

  C#

  •

  BSD 2-Clause "Simplified" License

  •0•1•0•0•Updated Jan 17, 2025Jan 17, 2025

• PNNL.DIA.utils

  Public
  **WORK IN PROGRESS** misc. functions for DIA proteomics data analysis and parsing to MSnSet objects

  R

  •

  Other

  •1•0•2•0•Updated Jan 14, 2025Jan 14, 2025

• DBSchema_DMS

  Public
  PRISM Data Management System database schema

  TSQL

  •3•3•0•0•Updated Jan 12, 2025Jan 12, 2025

• DLL-Version-Inspector

  Public
  This program inspects a .NET DLL or .Exe to determine the version. This allows a 32-bit .NET application to call this program via the command prompt to determine the version of a 64-bit DLL or Exe.

  C#

  •0•0•0•0•Updated Jan 11, 2025Jan 11, 2025

• MyEMSL-Reader

  Public
  MyEMSL Reader

  C#

  •0•2•0•0•Updated Dec 26, 2024Dec 26, 2024

• AScore

  Public
  The AScore program can process first-hits or synopsis files from MS-GF+, SEQUEST, or X!Tandem to compute confidence scores for the position of phosphorylated residues.

  mass-spectrometry

  C#

  •1•3•0•0•Updated Dec 22, 2024Dec 22, 2024

• Protein-Parsimony

  Public
  Program that implements a protein parsimony algorithm for grouping proteins with similar peptides.

  mass-spectrometry

  C#

  •0•0•1•0•Updated Dec 21, 2024Dec 21, 2024

• Mage

  Public
  The Mage suite of tools provide access to DMS files and metadata.

  C#

  •0•0•0•0•Updated Dec 20, 2024Dec 20, 2024

• AutoCCS

  Public
  Automated Collision Cross Section calculation software for ion mobility spectrometry-mass spectrometry

  mass-spectrometry

  Python

  •

  BSD 2-Clause "Simplified" License

  •1•8•1•0•Updated Dec 13, 2024Dec 13, 2024

• PHRP

  Public
  Converts a MS-GF+ .tsv search result file or an X!Tandem results file (XML format) into a series of tab-delimited text files, summarizing the results. It also supports results files from MaxQuant, MSAlign, TopPIC, MODa, MODPlus, and MSPathFinder, along with SEQUEST Synopsis/First Hits files.

  mass-spectrometry

  C#

  •0•0•0•0•Updated Dec 7, 2024Dec 7, 2024