Ecosyste.ms: Repos
An open API service providing repository metadata for many open source software ecosystems.
GitHub topics: mass-spectrometry
EMSL-Computing/CoreMS
CoreMS is a comprehensive mass spectrometry software framework
Language: Python - Size: 278 MB - Last synced: about 6 hours ago - Pushed: about 7 hours ago - Stars: 46 - Forks: 25
rformassspectrometry/QFeatures
Quantitative features for mass spectrometry data
Language: R - Size: 20.9 MB - Last synced: about 6 hours ago - Pushed: about 8 hours ago - Stars: 20 - Forks: 6
theGreatHerrLebert/rustims
A Framework for IMS-MS Raw Data Processing written in Rust and Python.
Language: Rust - Size: 36.9 MB - Last synced: about 8 hours ago - Pushed: 1 day ago - Stars: 4 - Forks: 1
mpecchi/gcms_data_analysis
Tool to analyze multiple GCMS qualitative tables
Language: Python - Size: 2.13 MB - Last synced: about 10 hours ago - Pushed: about 22 hours ago - Stars: 3 - Forks: 1
ipb-halle/MetFamily
Understanding metabolism is fundamental in biomedical and plant research and the identification and quantification of thousands of metabolites by mass spectrometry in modern metabolomics is a prerequisite for elucidating this area. However, the identification of metabolites is a major bottleneck in traditional approaches hampering advances. Here, we present a novel approach for the untargeted discovery of metabolite families offering a bird's eye view of metabolic regulation in comparative metabolomics. We implemented the presented methodology in the easy-to-use web application MetFamily to enable the analysis of comprehensive metabolomics studies for all researchers worldwide. MetFamily is available under http://msbi.ipb-halle.de/MetFamily/.
Language: R - Size: 21.9 MB - Last synced: about 9 hours ago - Pushed: about 11 hours ago - Stars: 8 - Forks: 8
524D/mzrecal
Recalibrate Mass Spectrometry data in mzML format
Language: Go - Size: 6.22 MB - Last synced: about 10 hours ago - Pushed: about 11 hours ago - Stars: 6 - Forks: 0
sorenwacker/ms-peakonly
Peak detection for untargeted metabolomics using Neural Network. High-level API based on peakonly by @Arseha.
Language: Jupyter Notebook - Size: 31.7 MB - Last synced: about 13 hours ago - Pushed: about 14 hours ago - Stars: 13 - Forks: 6
lifs-tools/jgoslin
Java implementation of the latest shorthand nomenclature.
Language: Java - Size: 18.9 MB - Last synced: about 13 hours ago - Pushed: about 14 hours ago - Stars: 4 - Forks: 0
matchms/matchms
Python library for processing (tandem) mass spectrometry data and for computing spectral similarities.
Language: Python - Size: 38 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 165 - Forks: 57
wfondrie/depthcharge
A deep learning toolkit for mass spectrometry
Language: Python - Size: 1.51 MB - Last synced: about 18 hours ago - Pushed: about 18 hours ago - Stars: 51 - Forks: 16
OpenChrom/openchrom
Visualization and Analysis of mass spectrometric and chromatographic data.
Language: Java - Size: 42.6 MB - Last synced: about 9 hours ago - Pushed: about 18 hours ago - Stars: 76 - Forks: 24
bigbio/quantms Fork of nf-core/quantms
Quantitative mass spectrometry workflow.
Language: Nextflow - Size: 46.9 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 17 - Forks: 6
fgcz/bfabricShiny
Manage life sciences data using R and b-fabric - a WSDL/REST interface and a tool box; main focus on MS data
Language: R - Size: 1.27 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 8 - Forks: 1
Vitek-Lab/MSstatsConvert
Converter functions for the MSstats package
Language: R - Size: 2.25 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 7 - Forks: 3
compomics/psm_utils
Common utilities for parsing and handling peptide-spectrum matches and search engine results in Python
Language: Python - Size: 104 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 20 - Forks: 6
yguitton/CP-Seeker
CP-Seeker is dedicated to the post-acquisition processing, visualization and analysis of ion signals from polychlorinated alkanes (PCAs) and related chemical families within chromatography–high resolution mass spectrometry (HRMS) data sets.
Language: C++ - Size: 1.78 GB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 0 - Forks: 0
hgb-bin-proteomics/MSAnnika_exporters
Export MS Annika crosslink results to different formats.
Language: Python - Size: 95.1 MB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 1 - Forks: 0
nf-core/quantms 📦
Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
Language: Nextflow - Size: 21.5 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 26 - Forks: 28
metgem/metgem
Calculation and visualization of molecular networks based on t-SNE algorithm
Language: Python - Size: 16.8 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 28 - Forks: 3
Nesvilab/philosopher
PeptideProphet, PTMProphet, ProteinProphet, iProphet, Abacus, and FDR filtering
Language: Go - Size: 651 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 108 - Forks: 17
wilhelm-lab/dlomix
Python framework for Deep Learning in Proteomics
Language: Python - Size: 271 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 19 - Forks: 9
acinostroza/TargetSearch
R package for the analysis of GC-MS metabolite profiling data. This git repository mirrors the TargetSearch git repository on bioconductor.
Language: R - Size: 993 KB - Last synced: 3 days ago - Pushed: 4 days ago - Stars: 4 - Forks: 0
lazear/sage
Proteomics search & quantification so fast that it feels like magic
Language: Rust - Size: 9.11 MB - Last synced: 2 days ago - Pushed: 4 days ago - Stars: 194 - Forks: 38
eugenemel/maven
Maven GUI: Metabolomics Analysis and Visualization Engine
Language: C++ - Size: 5.32 MB - Last synced: 4 days ago - Pushed: 5 days ago - Stars: 18 - Forks: 9
HassounLab/ESP
ESP model
Language: Python - Size: 125 MB - Last synced: 3 days ago - Pushed: 5 days ago - Stars: 1 - Forks: 0
eugenemel/maven_core
MAVEN: Core Libraries
Language: C++ - Size: 4.33 MB - Last synced: 4 days ago - Pushed: 5 days ago - Stars: 3 - Forks: 2
pmartR/pmartR
The pmartR R package provides functionality for quality control, normalization, exploratory data analysis, and statistical analysis of mass spectrometry (MS) omics data, in particular proteomic (either at the peptide or the protein level), lipidomic, and metabolomic data.
Language: R - Size: 78.8 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 36 - Forks: 16
ag-warscheid/autoprot
autoprot provides standardised, fast, and reliable proteomics data analysis while ensuring a high customisability needed to tailor the analysis pipeline to specific experimental strategies.
Language: Python - Size: 193 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 6 - Forks: 1
bigbio/pgt-pangenome
Protegenomics analysis based on Pangenome references
Language: Jupyter Notebook - Size: 569 MB - Last synced: 4 days ago - Pushed: 5 days ago - Stars: 0 - Forks: 0
sgibb/topdownrdata
Example data for the `topdown` R package
Language: R - Size: 117 MB - Last synced: 6 days ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0
sgibb/talk-odense-20171127
Example files for talk in Odense 2017
Language: HTML - Size: 14.7 MB - Last synced: 6 days ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0
fgcz/rawrr
Access Orbitrap data in R lang using C# mono assembly - bioconductor package
Language: R - Size: 3.09 MB - Last synced: 6 days ago - Pushed: 7 days ago - Stars: 50 - Forks: 7
CIRDLES/Tripoli
Tripoli imports raw mass spectrometer data files and supports interactive review and archiving of isotopic data. Tripoli facilitates visualization of temporal trends and scatter during measurement, statistically rigorous filtering of data, and calculation of statistical parameters.
Language: Java - Size: 40.9 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 8 - Forks: 12
JamesxX/ionio-illustrate
A Typst package for rendering and annotating mass spectrometric data
Language: Typst - Size: 3.87 MB - Last synced: 7 days ago - Pushed: 8 days ago - Stars: 3 - Forks: 0
fgcz/rawDiag
Brings Orbitrap mass spectrometry data to life; multi-platform, fast and colorful R package
Language: R - Size: 172 MB - Last synced: 7 days ago - Pushed: 8 days ago - Stars: 36 - Forks: 11
vmalnathnambiar/exfilms
A cross-platform, command line interface (CLI) tool to extract mass spectrometry (MS) data from mzML formatted files, with filtering capabilities.
Language: JavaScript - Size: 17.4 MB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 0 - Forks: 0
lgatto/MSnbase
Base Classes and Functions for Mass Spectrometry and Proteomics
Language: R - Size: 96.6 MB - Last synced: 6 days ago - Pushed: 8 days ago - Stars: 119 - Forks: 50
rformassspectrometry/Spectra
Low level infrastructure to handle MS spectra
Language: R - Size: 16.6 MB - Last synced: 8 days ago - Pushed: 9 days ago - Stars: 31 - Forks: 23
rformassspectrometry/MetaboCoreUtils
Core utilities for metabolomics.
Language: R - Size: 13.4 MB - Last synced: 25 days ago - Pushed: 25 days ago - Stars: 7 - Forks: 6
jeffsocal/mspredictr
A lightweight package for predicting peptide fragment mass values
Language: Rust - Size: 4.35 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 1 - Forks: 1
jeffsocal/msfastar
A light-weight FASTA reader and parser
Language: R - Size: 4.22 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 1 - Forks: 1
jeffsocal/msreadr
A simplified mass-spec data reader
Language: R - Size: 4.15 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 1 - Forks: 0
domdfcoding/pynist
PyMassSpec extension for searching mass spectra using NIST's Mass Spectrum Search Engine.
Language: C - Size: 24.3 MB - Last synced: 7 days ago - Pushed: 9 days ago - Stars: 18 - Forks: 2
MannLabs/alphabase
Infrastructure of AlphaX ecosystem
Language: Jupyter Notebook - Size: 39.4 MB - Last synced: 16 days ago - Pushed: 16 days ago - Stars: 23 - Forks: 7
UCLouvain-CBIO/LSTAT2340
Traitement statistique de données omiques
Language: HTML - Size: 21.9 MB - Last synced: 9 days ago - Pushed: 10 days ago - Stars: 0 - Forks: 0
mapio/jp2rt
A Java and Python package to Predict Retention Times
Language: Java - Size: 286 KB - Last synced: 6 days ago - Pushed: about 1 month ago - Stars: 3 - Forks: 0
Francis-B/Kiwi
Fast regex-based protein digestion and unique peptides finder tool
Language: Python - Size: 6.83 MB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 0 - Forks: 0
pymzml/pymzML
pymzML - an interface between Python and mzML Mass spectrometry Files
Language: Python - Size: 29.7 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 154 - Forks: 91
computational-metabolomics/msPurity
R-package - Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics
Language: HTML - Size: 12.8 MB - Last synced: 12 days ago - Pushed: 8 months ago - Stars: 15 - Forks: 4
Vitek-Lab/MSstatsTMT
R-based package for detecting differentially abundant proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling
Language: R - Size: 61.2 MB - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 26 - Forks: 13
PyProphet/pyprophet
PyProphet: Semi-supervised learning and scoring of OpenSWATH results.
Language: Python - Size: 45.4 MB - Last synced: 12 days ago - Pushed: 4 months ago - Stars: 27 - Forks: 21
snijderlab/stitch
Template-based assembly of proteomics short reads for de novo antibody sequencing and repertoire profiling
Language: C# - Size: 82.3 MB - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 16 - Forks: 3
xxao/pyeds Fork of thermofisherlsms/pyeds
Provides easy access to Thermo Discoverer platform results
Language: Python - Size: 47.3 MB - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 0 - Forks: 0
bigbio/py-pgatk
Python tools for proteogenomics analysis toolkit
Language: Python - Size: 125 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 9 - Forks: 11
PyMassSpec/PyMassSpec Fork of ma-bio21/pyms
Python Toolkit for Mass Spectrometry
Language: Python - Size: 72.6 MB - Last synced: 7 days ago - Pushed: 13 days ago - Stars: 31 - Forks: 10
domdfcoding/msp2lib
Convert an MSP file representing one or more Mass Spectra to a NIST MS Search user library.
Language: Python - Size: 292 KB - Last synced: 7 days ago - Pushed: 13 days ago - Stars: 1 - Forks: 1
lifs-tools/pygoslin
Python implementation of parsers for the Grammars on succinct lipid nomenclature (Goslin).
Language: Python - Size: 9.73 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 3 - Forks: 2
PyMassSpec/PyMassSpec-Plot
Plotting extension for PyMassSpec.
Language: Python - Size: 7.61 MB - Last synced: 12 days ago - Pushed: 13 days ago - Stars: 0 - Forks: 1
PyMassSpec/mh_utils
Utilities for handing ancillary files produced by MassHunter.
Language: Python - Size: 736 KB - Last synced: 7 days ago - Pushed: 13 days ago - Stars: 4 - Forks: 0
HUPO-PSI/psi-ms-CV
HUPO-PSI mass spectrometry CV
Language: Python - Size: 82.6 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 26 - Forks: 33
phenomecentre/peakPantheR
On-instrument and post-acquisition targeted feature extraction
Language: R - Size: 4.51 MB - Last synced: 14 days ago - Pushed: 14 days ago - Stars: 12 - Forks: 1
RECETOX/RIAssigner
RIAssigner is a python tool for retention index (RI) computation for GC-MS data.
Language: Python - Size: 8.54 MB - Last synced: 25 days ago - Pushed: 3 months ago - Stars: 4 - Forks: 6
smith-chem-wisc/mzLib
Library for mass spectrometry projects
Language: C# - Size: 201 MB - Last synced: 12 days ago - Pushed: 14 days ago - Stars: 25 - Forks: 30
RECETOX/recetox-aplcms Fork of tianwei-yu/apLCMS
This is a custom fork of apLCMS containing adaptations for large scale studies.
Language: R - Size: 24.4 MB - Last synced: 14 days ago - Pushed: 14 days ago - Stars: 4 - Forks: 7
tornikeo/cudams
CUDA-accelerated MatchMS
Language: Jupyter Notebook - Size: 15.5 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 0 - Forks: 0
rickhelmus/patRoon
Workflow solutions for mass-spectrometry based non-target analysis.
Language: R - Size: 551 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 54 - Forks: 17
CooperstoneLab/MS2extract
R package to create in-house MS/MS compound libraries
Language: R - Size: 38.3 MB - Last synced: 15 days ago - Pushed: 15 days ago - Stars: 5 - Forks: 0
Omicometrics/pypls
Implementation of PLS-DA and OPLS-DA for high dimensional data, like MS in metabolomics.
Language: Python - Size: 146 KB - Last synced: 15 days ago - Pushed: 16 days ago - Stars: 19 - Forks: 3
abhijitju06/JUMPt-Version-1.0.0
JUMPt Version 1.0.0
Language: MATLAB - Size: 1.95 MB - Last synced: 15 days ago - Pushed: 3 months ago - Stars: 1 - Forks: 0
bittremieux/spectrum_utils
Python package for efficient mass spectrometry data processing and visualization
Language: Python - Size: 3.48 MB - Last synced: 16 days ago - Pushed: 17 days ago - Stars: 124 - Forks: 21
cgohlke/molmass
Molecular mass calculations
Language: Python - Size: 385 KB - Last synced: 10 days ago - Pushed: 8 months ago - Stars: 48 - Forks: 12
MetaboHUB-MetaToul-FluxoMet/RTMet
RTMet is a data workflow to process FIA-MS data coming from a fermenter, find metabolites and fluxes, and send a feedback command to the fermenter.
Language: R - Size: 409 KB - Last synced: 16 days ago - Pushed: 16 days ago - Stars: 1 - Forks: 0
lifs-tools/goslin
Goslin is the Grammar on succinct lipid nomenclature.
Language: ANTLR - Size: 7.17 MB - Last synced: 15 days ago - Pushed: 17 days ago - Stars: 10 - Forks: 1
MannLabs/alphatims
An open-source Python package for efficient accession and visualization of Bruker TimsTOF raw data from the Mann Labs at the Max Planck Institute of Biochemistry.
Language: Python - Size: 96.9 MB - Last synced: 15 days ago - Pushed: 8 months ago - Stars: 75 - Forks: 24
rformassspectrometry/MsCoreUtils
Core Utils for Mass Spectrometry Data
Language: R - Size: 12.5 MB - Last synced: 17 days ago - Pushed: 17 days ago - Stars: 16 - Forks: 11
pgarrett-scripps/peptacular
A spectacularly simple package for working with peptide sequences.
Language: Python - Size: 11.3 MB - Last synced: 17 days ago - Pushed: 18 days ago - Stars: 8 - Forks: 0
lifs-tools/cppgoslin
C++ implementation of parsers for the Grammars on succinct lipid nomenclature (Goslin).
Language: C++ - Size: 9.17 MB - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 0 - Forks: 0
bigbio/sdrf-pipelines
A repository to convert SDRF proteomics files into pipelines config files
Language: Python - Size: 2.47 MB - Last synced: 1 day ago - Pushed: about 1 month ago - Stars: 14 - Forks: 20
mobiusklein/brainpy
A Python implementation of Baffling Recursive Algorithm for Isotopic distributioN calculations
Language: Python - Size: 1.31 MB - Last synced: 8 days ago - Pushed: 5 months ago - Stars: 19 - Forks: 10
yufree/rmwf
Reproducilble Metabolomics Workflow
Language: R - Size: 527 MB - Last synced: 20 days ago - Pushed: 21 days ago - Stars: 7 - Forks: 2
yufree/pmd
Paired Mass Distance(PMD) analysis for GC/LC-MS based nontarget analysis
Language: R - Size: 78.1 MB - Last synced: 20 days ago - Pushed: 21 days ago - Stars: 9 - Forks: 0
protViz/quantable
Streamlines descriptive analysis of quantitative mass spectrometry data.
Language: R - Size: 7.38 MB - Last synced: 20 days ago - Pushed: over 2 years ago - Stars: 11 - Forks: 3
MetaSys-LISBP/IsoCor
IsoCor: Isotope Correction for mass spectrometry labeling experiments
Language: Python - Size: 2.39 MB - Last synced: 20 days ago - Pushed: 6 months ago - Stars: 24 - Forks: 8
xieguigang/mzkit
Data toolkits for processing NMR, MALDI MSI, MALDI single cell, Raman Spectroscopy, LC-MS and GC-MS raw data, chemoinformatics data analysis and data visualization.
Language: Visual Basic .NET - Size: 487 MB - Last synced: 22 days ago - Pushed: 24 days ago - Stars: 44 - Forks: 14
Progklui/vwaFloKlui
Vorschwissenschaftliche Arbeit zum Thema "Direkte Analyse von Chlorophyllkataboliten"
Language: Jupyter Notebook - Size: 157 MB - Last synced: 21 days ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0
MannLabs/alphapept
A modular, python-based framework for mass spectrometry. Powered by nbdev.
Language: HTML - Size: 204 MB - Last synced: 19 days ago - Pushed: 19 days ago - Stars: 154 - Forks: 28
compomics/moFF
A modest Feature Finder (moFF) to extract MS1 intensities from Thermo raw file
Language: Python - Size: 5.73 MB - Last synced: 22 days ago - Pushed: about 3 years ago - Stars: 32 - Forks: 11
RECETOX/galaxytools
Set of Galaxy tool wrappers developed at RECETOX
Language: Python - Size: 46.4 MB - Last synced: 25 days ago - Pushed: 27 days ago - Stars: 12 - Forks: 12
anuragraj/PgxSAVy
A tool for quality control and annotation of variant peptides after FDR in proteogenomics
Language: Perl - Size: 1.98 MB - Last synced: 23 days ago - Pushed: 4 months ago - Stars: 0 - Forks: 0
mayankmtg/MassSpecPeakDetection
Peak Detection algorithm refine for testing the number of peaks based on different approaches
Language: Python - Size: 25.7 MB - Last synced: 23 days ago - Pushed: almost 6 years ago - Stars: 1 - Forks: 0
EMSL-Computing/IonToolPack
A software tool for omics-agnostic automated quality control of mass spectrometry data.
Language: Python - Size: 460 MB - Last synced: 23 days ago - Pushed: 23 days ago - Stars: 0 - Forks: 0
Nesvilab/FragPipe
A cross-platform Graphical User Interface (GUI) for running MSFragger and Philosopher - powered pipeline for comprehensive analysis of shotgun proteomics data
Language: Java - Size: 2.57 GB - Last synced: 25 days ago - Pushed: 26 days ago - Stars: 160 - Forks: 35
snijderlab/rustyms
A rust library for parsing Pro Forma peptides and matching them against MS spectra
Language: Rust - Size: 73.1 MB - Last synced: 26 days ago - Pushed: 27 days ago - Stars: 10 - Forks: 2
UCLouvain-CBIO/scp
Single cell proteomics data processing
Language: R - Size: 64.2 MB - Last synced: 26 days ago - Pushed: 26 days ago - Stars: 18 - Forks: 0
OpenMS/OpenMS
The codebase of the OpenMS project
Language: C++ - Size: 609 MB - Last synced: 25 days ago - Pushed: 26 days ago - Stars: 455 - Forks: 306
nf-core/metaboigniter
Pre-processing of mass spectrometry-based metabolomics data with quantification and identification based on MS1 and MS2 data.
Language: Nextflow - Size: 46.1 MB - Last synced: 26 days ago - Pushed: 26 days ago - Stars: 15 - Forks: 14
mgleeming/synthedia
Create synthetic DIA LC-MS/MS for proteomics experiments
Language: Python - Size: 2.4 MB - Last synced: 16 days ago - Pushed: about 1 year ago - Stars: 9 - Forks: 0
sgibb/MALDIquant
Quantitative Analysis of Mass Spectrometry Data
Language: R - Size: 1.71 MB - Last synced: 6 days ago - Pushed: 4 months ago - Stars: 57 - Forks: 25
griquelme/tidyms
TidyMS: Tools for working with MS data in untargeted metabolomics
Language: Python - Size: 30.3 MB - Last synced: about 1 month ago - Pushed: 2 months ago - Stars: 49 - Forks: 11
NMGRL/pychron
Data acquisition and processing framework for Ar-Ar geochronology and noble gas mass spectrometry
Language: Python - Size: 112 MB - Last synced: 29 days ago - Pushed: 29 days ago - Stars: 26 - Forks: 26
