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Computational Mass Spectrometry @ Pacific Northwest National Laboratory (@PNNL-Comp-Mass-Spec)

PNNL-Comp-Mass-Spec

Stars
357
Global Org. Rank 28,966 (Top 10 %)
Registered over 10 years ago
Most used languages

C#
52.6 %

Python
8.2 %

C++
5.2 %

Visual Basic .NET 5.2 %

R
5.2 %

Jupyter Notebook
4.1 %

Visual Basic 4.1 %

HTML
4.1 %

PLpgSQL 2.1 %

JavaScript
2.1 %

TSQL 2.1 %

VBA 2.1 %

TeX
1.0 %

PHP
1.0 %

CSS
1.0 %
Location 🇺🇸 United States
Country Total Rank 19,793
Country Ranking

VBA 25

Visual Basic .NET 45

TSQL 158

Visual Basic 167

PLpgSQL 206

C#
807

TeX
1,528

R
2,908

C++
9,227

HTML
9,989

Thermo-Raw-File-Reader

.NET DLL wrapper for reading Thermo .Raw files. Uses ThermoFisher.CommonCore NuGet packages provided by Thermo Fisher Scientific

Informed-Proteomics

Top down / bottom up, MS/MS analysis tool for DDA and DIA mass spectrometry data

LIQUID

Software tool for identifying lipids in LC-MS/MS-based lipidomics data

DeconTools

Used to deisotope mass spectra and to detect features from mass spectrometry data using observed isotopic signatures.

MASIC

MASIC generates selected ion chromatograms (SICs) for all of the parent ions chosen for fragmentation in an LC-MS/MS analysis, characterizing the peak(s) in each SIC, computing peak statistics including elution time of the peak apex, peak area, and peak signal/noise. It can also extract reporter ion abundances (e.g. iTRAQ or TMT).

DB-Schema-Export-Tool

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.

Molecular-Weight-Calculator-VB6

Molecular Weight Calculator (MWTWin): Graphical program written in VB6 with numerous mass calculation utilities.

Molecular-Weight-Calculator-DLL

The Molecular Weight Calculator can be used to calculate the molecular weight and percent composition of chemical formulas and amino acids (peptides). It includes several other utility modules and is available as both a GUI version and a C# DLL version.

MS-File-Info-Scanner

Examines a series of MS data files (or data directories) and extracts the acquisition start and end times, number of spectra, and the total size of the data. In addition, it can create 2D-plot graphics of the m/z values vs. time for QA purposes.

AutoCCS

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

LCMS-Spectator

LCMS raw data and MS-GF+ results viewer

Formultitude

Software for the assignment of low weight molecular formulas from high-resolution mass spectra.

proteomics-data-analysis-tutorial

A comprehensive tutorial for proteomics data analysis in R that utilizes packages developed by researchers at PNNL and from Bioconductor.

Venn-Diagram-Plotter

The Venn Diagram Plotter draws correctly proportioned and positioned two and three circle Venn diagrams (aka Euler diagrams) whose colors can be customized and the diagrams copied to the clipboard or saved to disk.

Visual Basic .NET

protein-coverage-summarizer

Computes the percent of the residues in each protein sequence that have been identified, based on a list of identified peptides. A graphical user interface (GUI) is provided to allow the user to select the input files, set the options, and browse the coverage results.

Mzid-To-Tsv-Converter

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

DeconEngineV2

The DeconEngine includes routines for deconvoluting (deisotoping) observed isotopic signatures in mass spectrometry data to detect features. The releases include Zip files with DeconMSn.exe

uimfpy

UIMF python library

Protein-Digestion-Simulator

Performs validation, transformation, and in-silico digestion of text files containing protein or peptide sequences (FASTA format or delimited text)

InfernoRDN

InfernoRDN can perform various downstream analyses on large scale datasets from proteomics and microarrays

RomicsProcessor

R package that provides a structured R object to store and analyze omics data

PSI-Interface

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

DBSchema_PgSQL_DMS

PRISM Data Management System PostgreSQL database schema

LCMSNet

LCMSNet software for instrument control

Uniprot-DAT-File-Parser

This program can read a Uniprot .Dat file and parse out the information for each entry, creating a tab delimited text file or a FASTA file.

Visual Basic .NET

AqMD3-Acquisition-Console

Acquisition software for the Acqiris SA220P digitizer card

Thermo-FAIMS-to-MzML

Converts a Thermo .raw file with FAIMS scans into a series of .mzML files, creating one .mzML file for each FAIMS compensation voltage (CV) value.

ChemstationMSFileReader

Allows for reading Agilent Chemstation .D folders using Dot.NET

DMS-Analysis-Manager

DMS Analysis Tool Manager

DBSchema_DMS

PRISM Data Management System database schema

MS-Data-File-Reader

A VB.NET DLL that can read mass spectrometry data from four file formats: mzXML, mzData, concatenated .dta files (_dta.txt), and Mascot Generic Format files (.mgf)

DBSchema_MTS

PRISM Mass and Time Tag System database schema

MultiAlign

Aligns multiple LC-MS datasets to one another after which LC-MS features can be matched to a database of peptides (typically an AMT tag database)

Proteowizard-Wrapper

C# classes that can be used to interface with the ProteoWizard libraries

TopPICR

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

Kaiko

deep learning-based de novo peptide sequencing tool

MetabolomicsCCS

This is a the code and data for a website created to display collision cross section data for metabolites and small molecules

Fasta-File-Splitter

The FASTA File Splitter program can be used to split apart a protein FASTA file into a number of sections. Although the splitting is random, each section will have a nearly identical number of residues.

SQLServer-Stored-Procedure-Converter

Converts SQL Server stored procedures to PostgreSQL compatible stored procedures

BP-Quant

MyEMSL-Reader

MzidMerger

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

SimELIT

multi-physics and multi-scale simulation software for mass spectrometry

Q4SRM

Q4SRM: Quality assessment for QQQ SRM

PRISM-Class-Library

The PRISM Class Library is a collection of routines used by many of the software tools that support the Data Management System at PNNL.

MyEMSL-MTS-File-Cache-Manager

MTS manager for retrieving files from MyEMSL

BrukerDataReader

Bruker data reader

Step-Field-CCS

Step field collisional cross section (CCS) calculation

MSCC

Multidimensional Stoichiometric Compound Classification

DeepKS

bsf-py

Python wrapper for Blazing Signature Filter

AmpsSDK

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

LipidMiniOn

Shiny interface for the Lipid Mining and Ontology (Lipid Mini-On) tool, which uses the Rodin R package

GlyQ-IQ

GlyQ-IQ is a program that performs a targeted, chromatographic centric search of mass spectral data for glycans.

Tissue_Classification

Jupyter Notebook

Multidimensional-Peak-Finding

Finds 3D XIC features across LC, m/z, and drift time dimensions

IMS-Drift-Time-Aligner

Processes IMS data in a UIMF file to align all frames to a base frame, adjusting the observed drift times of each frame to align with the base frame.

IMS-Informed-Library

ImsInformed is a .NET class library that provides target identification workflows for peptides and metabolites alike in IMS experiment runs.

BioPython_Scripts

BioPython scripts for conversion of GBK files or DNA-based FASTA files to protein FASTA files

OBO-Data-Converter

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

LINCS-Finder

a web app to find the most interesting signatures from LINCS L1000

DMS-Website

PHRP

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.

Buzzard

Utility for manually and automatically adding datasets to DMS

Rodin

R package used by Lipid Mini-On to create ontology bins and perform lipid enrichment analysis.

UIMF-Viewer

Visualization software for IMS data stored in a UIMF file

DMS-Capture-Task-Manager

DMS Capture Task Manager

Thermo-Peak-Data-Exporter

Extracts peak intensity data from each scan in a Thermo raw file, and writes that data to a tab-delimited text file.

Fasta-Organism-Filter

Reads a protein FASTA file and filters the proteins by organism name, protein name, or taxonomy ID to create a new, filtered file.

LIPID-Split

Splits lipid annotation names by fatty acid. Adds total number of chain carbons and double bonds as new columns.

MetaboliteValidation

This is a simple c# console program to validate the data from Erin's Metabolite ccs

DL-Batch-Correction

Jupyter Notebook

CRNT4SBML

Uses chemical reaction network theory to evaluate whether a system encoded by SBML could be bistable

PNNL.DMS.utils

Tools to interface with PNNL's DMS in R

OxyDataPlotter

The OxyDataPlotter library includes a WinForms control with a customizable instance of OxyPlot.

Visual Basic .NET

LC-IMS-MS-Feature-Finder

Finds LC-IMS-MS features using deisotoped features from DeconTools

Validate-Fasta-File

Parses a FASTA file (with protein name and sequence information) to check for valid text. Also returns protein and residue stats.

UIMF-Library

Used to create, modify and extract data from UIMF files, which are SQLite databases of mass spectrometry data acquired at Pacific Northwest National Laboratory (PNNL)

PIXIE

ImsMetabolitesFinder searches for the presence of a target molecule in a UIMF file. The target mobility(K0) and cross sectional area(A) can be computed with varying drift tube voltages

proteinisletplotter

Sipper

Used to automatically detect and quantify partially labeled C13 peptides in a mass spectrometry dataset.

BSF_publication

All the data and materials for the publication about the Blazing Signature Filter

Jupyter Notebook

Kaiko_Publication

all the materials for the publication about the Kaiko

Jupyter Notebook

bsf-core

C++ library of Blazing Signature Filter

VIPER

VIPER (Visual Inspection of Peak/Elution Relationships) can be used to visualize and characterize the features detected during LC-MS analyses.

PeptideListToXML

The PeptideListToXML application reads a tab-delimited text file created by the Peptide Hit Results Processor (PHRP) and creates a PepXML with the appropriate information.

LipidFDR

Python scripts of SVM model training and testing used in a publication entitled 'A generalizable method for false-discovery rate estimation in mass spectrometry-based lipidomics'

PepAligner

The PepAligner program can read a file containing peptides and align them to a file of protein sequences (.Fasta or delimited text) using Smith-Waterman alignment.

R_skills_assessment

Atreyu

Ion mobility mass spectrometry data viewer and extractor, targeted toward PNNL's UIMF files

APE-DLL

The APE DLL is a library of methods used by the APE GUI to apply a series of data transformations to data stored in a SQLite database. The set of transformations is called a Workflow, and is composed of sequential steps to apply.

Visual Basic .NET

Protein-Sequence-Motif-Extractor

Reads a FASTA file or tab delimited file containing protein sequences, then looks for the specified motif in each protein sequence. Results are stored in a new file containing the regions of the protein that contain the specified motif.

Visual Basic .NET

PNNL-Comp-Mass-Spec.github.io

Markdown files displayed at https://pnnl-comp-mass-spec.github.io/

DataFilter-DLL

Butterworth filter, Moving Window Average filter, and Savitzky Golay filter

MASIC-Results-Merger

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

SAIS-CSharp

Suffix array, induced sorting library. Source from https://sites.google.com/site/yuta256/sais, with updated project and framework configuration

Peptide-Fragmentation-Modeller

The Peptide Fragmentation Modeller is a command-line utility reads that reads in a text file of peptide sequences and generates the theoretical fragmentation pattern for each, outputting the results in a single concatenated DTA file, or in separate .Dta files. The ion intensity values are not predicted values; instead, b, c, y, and z ions are assigned an intensity of 100; while a ions and neutral loss ions receive an intensity of 20.

PNNL-Biodiversity-Library-Plugin

The PNNL Biodiversity Plugin is a software tool for Skyline and is designed to allow pathway-centric browsing of peptides previously identified by LC-MS/MS. The plugin is designed to assist in SRM assay design or DIA data analysis. Users select an organism and biological pathway of interest, then the plugin shows information about the associated peptides. In total the Biodiversity Library catalogs MS/MS spectra from 2 million peptides and 200,000 proteins from over 118 distict organisms. Users can optionally import peptide data for selected proteins into Skyline to extend their local copy of the Biodiversity Library.

MotrpacRatTrainingPhysiologyData

Data and analysis results for the MoTrPAC PASS1B rat physiology manuscript

PNNL-PreProcessor

Distribution binaries for the PNNL PreProcessor