Repositories list

• 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 Mar 10, 2025Mar 10, 2025

• DMS-Analysis-Manager

  Public
  DMS Analysis Tool Manager

  C#

  •

  BSD 2-Clause "Simplified" License

  •0•3•0•0•Updated Mar 10, 2025Mar 10, 2025

• MASIC-Results-Merger

  Public
  Merges the contents of a tab-delimited text file with peptide search results (e.g. from MS-GF+, MaxQuant, or X!Tandem) with the corresponding MASIC results files, appending the relevant MASIC stats for each PSM. Also supports reporter ion abundances.

  mass-spectrometry

  C#

  •0•2•1•0•Updated Mar 7, 2025Mar 7, 2025

• DBSchema_PgSQL_DMS

  Public
  PRISM Data Management System PostgreSQL database schema

  PLpgSQL

  •0•3•0•0•Updated Mar 5, 2025Mar 5, 2025

• MSnSet.utils

  Public
  custom wrappers of frequently used R code

  R

  •8•7•3•1•Updated Mar 4, 2025Mar 4, 2025

• OBO-Data-Converter

  Public
  Utility for converting ontology OBO files to a tab-delimited text file.

  ontologyobo

  C#

  •0•1•0•0•Updated Feb 27, 2025Feb 27, 2025

• DMS-Capture-Task-Manager

  Public
  DMS Capture Task Manager

  C#

  •

  BSD 2-Clause "Simplified" License

  •0•1•0•0•Updated Feb 26, 2025Feb 26, 2025

• Parameter-File-Editor

  Public
  DLL for retrieving parameter files from DMS

  Visual Basic .NET

  •0•0•0•0•Updated Feb 20, 2025Feb 20, 2025

• mediawiki-extensions-CirrusSearch

  Public
  🔍 Mirror of https://gerrit.wikimedia.org/g/mediawiki/extensions/CirrusSearch. See https://www.mediawiki.org/wiki/Developer_access for contributing.

  PHP

  •

  GNU General Public License v2.0

  •20•0•0•1•Updated Feb 19, 2025Feb 19, 2025

• ROSMAP103_TopDown

  Public
  R

  •0•0•0•0•Updated Feb 19, 2025Feb 19, 2025

• DMS-Website

  Public
  DMS Website

  PHP

  •0•1•0•1•Updated Feb 19, 2025Feb 19, 2025

• DataPackage-Archive-Manager

  Public
  DataPackage Archive Manager

  C#

  •0•0•0•0•Updated Feb 15, 2025Feb 15, 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 14, 2025Feb 14, 2025

• Mzid-To-Tsv-Converter

  Public
  Converts an mzIdentML created by MS-GF+ to a tab-delimited text file.

  mass-spectrometrymzidentmlmzid

  C#

  •2•6•3•0•Updated Feb 12, 2025Feb 12, 2025

• MzidMerger

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

  mass-spectrometrymzidentmlmzid

  C#

  •0•3•0•0•Updated Feb 12, 2025Feb 12, 2025

• 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 11, 2025Feb 11, 2025

• PNNL-PreProcessor

  Public
  Distribution binaries for the PNNL PreProcessor

  0•3•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•6•2•Updated Jan 29, 2025Jan 29, 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•14•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•5•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•3•1•2•Updated Jan 22, 2025Jan 22, 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

• PNNL.DIA.utils

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

  R

  •

  Other

  •1•0•3•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