Ecosyste.ms: Repos
An open API service providing repository metadata for many open source software ecosystems.
GitHub topics: metabolomics
lifs-tools/jgoslin
Java implementation of the latest shorthand nomenclature.
Language: Java - Size: 18.9 MB - Last synced: about 2 hours ago - Pushed: about 3 hours ago - Stars: 4 - Forks: 0
MoTrPAC/MotrpacBicQC
R package for the MoTrPAC community
Language: R - Size: 3.61 MB - Last synced: about 3 hours ago - Pushed: about 4 hours ago - Stars: 8 - Forks: 4
omicsEye/massSight
An R package for the alignment and scaling of LC-MS metabolomics data
Language: R - Size: 13.5 MB - Last synced: about 3 hours ago - Pushed: about 4 hours ago - Stars: 2 - Forks: 0
rformassspectrometry/Spectra
Low level infrastructure to handle MS spectra
Language: R - Size: 19.2 MB - Last synced: about 10 hours ago - Pushed: about 11 hours ago - Stars: 31 - Forks: 23
lifs-tools/goslin-webapp
Web application and REST Api for parsers for the Grammars on succinct lipid nomenclature (Goslin).
Language: Java - Size: 1.26 MB - Last synced: about 9 hours ago - Pushed: about 11 hours ago - Stars: 1 - Forks: 0
lifs-tools/pygoslin
Python implementation of parsers for the Grammars on succinct lipid nomenclature (Goslin).
Language: Python - Size: 9.77 MB - Last synced: about 5 hours ago - Pushed: about 11 hours ago - Stars: 3 - Forks: 2
lifs-tools/goslin
Goslin is the Grammar on succinct lipid nomenclature.
Language: ANTLR - Size: 7.2 MB - Last synced: about 6 hours ago - Pushed: about 11 hours ago - Stars: 10 - Forks: 1
metgem/metgem
Calculation and visualization of molecular networks based on t-SNE algorithm
Language: Python - Size: 16.9 MB - Last synced: about 12 hours ago - Pushed: about 14 hours ago - Stars: 28 - Forks: 3
hancockinformatics/MetaBridgeShiny
Repository for the MetaBridge Shiny app.
Language: R - Size: 115 MB - Last synced: about 15 hours ago - Pushed: 1 day ago - Stars: 2 - Forks: 0
EBI-Metabolights/SAFERnmr
Language: R - Size: 69.3 MB - Last synced: about 15 hours ago - Pushed: 1 day ago - Stars: 3 - Forks: 2
yufree/rmwf
Reproducilble Metabolomics Workflow
Language: R - Size: 527 MB - Last synced: about 16 hours ago - Pushed: 1 day ago - Stars: 7 - Forks: 2
lucinamay/biosynfoni
a *biosynformatic* fingerprint to explore natural product distance and diversity
Language: Python - Size: 11.1 MB - Last synced: about 16 hours ago - Pushed: 1 day ago - Stars: 8 - Forks: 1
mapp-metabolomics-unit/met-annot-unifier
A Python package to handle metabolite annotation tables (GNPS, ISDB and Sirius)
Language: Python - Size: 4.1 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 0 - Forks: 0
rformassspectrometry/MetaboAnnotation
High level functionality to support and simplify metabolomics data annotation.
Language: R - Size: 12.4 MB - Last synced: about 23 hours ago - Pushed: 1 day ago - Stars: 11 - Forks: 9
Melclic/intersectomics
Package to study time series (or other series) multi-omics patterns of expresssion with replicates
Language: Python - Size: 1.52 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 0 - Forks: 0
microbiomedata/nmdc-schema
National Microbiome Data Collaborative (NMDC) unified data model
Language: Python - Size: 115 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 27 - Forks: 8
CNIC-Proteomics/TurboPutative-web
Language: HTML - Size: 231 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 0 - Forks: 0
lifs-tools/cppgoslin
C++ implementation of parsers for the Grammars on succinct lipid nomenclature (Goslin).
Language: C++ - Size: 9.18 MB - Last synced: about 5 hours ago - Pushed: 2 days ago - Stars: 0 - Forks: 0
JuBiotech/peak-performance
A Python toolbox for Bayesian inference of peak areas.
Language: Python - Size: 559 MB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 1 - Forks: 0
Metaboverse/Metaboverse
Visualization and analysis platform for metabolic data and network pattern recognition
Language: JavaScript - Size: 511 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 38 - Forks: 6
AHuffmyer/SymbioticIntegration
Symbiotic nutritional exchange in coral larvae under thermal stress
Size: 171 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 0 - Forks: 0
rformassspectrometry/QFeatures
Quantitative features for mass spectrometry data
Language: R - Size: 21.4 MB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 21 - Forks: 6
enpadasi/Ontology-for-Nutritional-Studies
The Ontology for Nutritional Studies (ONS) has been developed as part of the ENPADASI European project (http://www.enpadasi.eu/) with the aim to define a common language and building ontologies for nutritional studies.
Size: 15.7 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 10 - Forks: 5
jorainer/xcmsTutorials
Tutorials and workshops describing LC-MS(/MS) data pre-processing and analysis using the xcms Bioconductor package
Language: TeX - Size: 33.7 MB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 5 - Forks: 1
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: 6 days ago - Pushed: 6 days ago - Stars: 15 - Forks: 3
wfondrie/depthcharge
A deep learning toolkit for mass spectrometry
Language: Python - Size: 1.29 MB - Last synced: 6 days ago - Pushed: 7 days ago - Stars: 51 - Forks: 16
sirius-ms/sirius
SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)
Language: Java - Size: 44.2 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 75 - Forks: 17
Meredith-Lab/volcalc
volcalc: Calculate Volatility of Chemical Compounds
Language: R - Size: 4.6 MB - Last synced: 6 days ago - Pushed: 7 days ago - Stars: 4 - Forks: 1
scibiome/meteor
`MeTEor` is an R Shiny application that offers the possibility to explore longitudinal metabolomics data. For this purpose, a variety of statistical analysis and visualization methods are implemented in MeTEor to help the user to get a quick overview of the data.
Language: R - Size: 19.4 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 5 - Forks: 0
cbib/DIMet
Differential analysis of targeted Isotope-labeled Metabolomics data
Language: Python - Size: 475 KB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 3 - Forks: 2
EBI-Metabolights/metabolights-editor
MetaboLights Online Editor (MOE) is a Single Page Application (SPA) built upon Angular 7, and Redux frameworks. MOE provides MetaboLights users and curators with an intuitive and easy to use interface to create, edit and annotate their studies online.
Language: TypeScript - Size: 4.22 MB - Last synced: 6 days ago - Pushed: 7 days ago - Stars: 3 - Forks: 1
plyush1993/OUKS
🔴OUKS🔵 Omics Untargeted Key Script
Language: R - Size: 30.4 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 8 - Forks: 2
EMSL-Computing/CoreMS
CoreMS is a comprehensive mass spectrometry software framework
Language: Python - Size: 278 MB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 46 - Forks: 25
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: 8 days ago - Pushed: 8 days ago - Stars: 13 - Forks: 6
xieguigang/mesh
MSdata expression matrix simulator for test metabolomics analysis pipeline
Language: HTML - Size: 65.5 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 6 - Forks: 2
BAMeScience/fiora
Fiora is an in silico fragmentation algorithm for small compounds and produces simulated tandem mass spectra (MS/MS). The framework uses a graph neural network as the core module and edge prediction to identify likely bond cleavages and fragment ion intensities.
Language: Jupyter Notebook - Size: 36.5 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 14 - Forks: 2
pcastellanoescuder/fobitools
:package: Tools for Manipulating FOBI Ontology
Language: R - Size: 19.2 MB - Last synced: 3 days ago - Pushed: 10 days ago - Stars: 1 - Forks: 3
tornikeo/cudams
CUDA-accelerated MatchMS
Language: Jupyter Notebook - Size: 15.5 MB - Last synced: 10 days ago - Pushed: 11 days ago - Stars: 0 - Forks: 0
PangeAI/cudams
GPU accelerated MatchMS
Language: Jupyter Notebook - Size: 4.35 MB - Last synced: 10 days ago - Pushed: 11 days ago - Stars: 0 - Forks: 0
eugenemel/maven
Maven GUI: Metabolomics Analysis and Visualization Engine
Language: C++ - Size: 5.32 MB - Last synced: 12 days ago - Pushed: 13 days ago - Stars: 18 - Forks: 9
eugenemel/maven_core
MAVEN: Core Libraries
Language: C++ - Size: 4.33 MB - Last synced: 12 days ago - Pushed: 13 days ago - Stars: 3 - Forks: 2
matchms/matchms
Python library for processing (tandem) mass spectrometry data and for computing spectral similarities.
Language: Python - Size: 38 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 165 - Forks: 57
pnnl/isicle
In silico chemical library engine for high-accuracy chemical property prediction
Language: Python - Size: 19.7 MB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 57 - Forks: 19
Karnovsky-Lab/DNEA
DNEA is an R package to construct data-driven biological networks from -omics data.
Language: R - Size: 45.1 MB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 0 - Forks: 0
opencobra/cobratoolbox
The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
Language: MATLAB - Size: 1.02 GB - Last synced: 15 days ago - Pushed: 15 days ago - Stars: 237 - Forks: 303
2n3m/2n3m
Biomedicine, Pharma, Life Science, IT Consulting
Size: 68.4 KB - Last synced: 20 days ago - Pushed: 20 days ago - Stars: 0 - Forks: 0
nara3m/nara3m
Nara Marella
Size: 30.3 KB - Last synced: 20 days ago - Pushed: 20 days ago - Stars: 0 - Forks: 0
p2m2/EP2M2
Metabolomics target analyzes manager
Language: Vue - Size: 8.04 MB - Last synced: 20 days ago - Pushed: 20 days ago - Stars: 1 - Forks: 1
yufree/metaworkflow
Online workflow guidelines for metabolomics
Language: TeX - Size: 33.2 MB - Last synced: 21 days ago - Pushed: 21 days ago - Stars: 23 - Forks: 10
phenomecentre/peakPantheR
On-instrument and post-acquisition targeted feature extraction
Language: R - Size: 4.51 MB - Last synced: 22 days ago - Pushed: 22 days ago - Stars: 12 - Forks: 1
CooperstoneLab/MS2extract
R package to create in-house MS/MS compound libraries
Language: R - Size: 38.3 MB - Last synced: 23 days ago - Pushed: 23 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: 23 days ago - Pushed: 24 days ago - Stars: 19 - Forks: 3
glasgowcompbio/vimms
A programmable and modular LC/MS simulator in Python
Language: Python - Size: 235 MB - Last synced: 23 days ago - Pushed: 24 days ago - Stars: 17 - Forks: 7
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: 24 days ago - Pushed: 24 days ago - Stars: 1 - Forks: 0
rformassspectrometry/MsCoreUtils
Core Utils for Mass Spectrometry Data
Language: R - Size: 12.5 MB - Last synced: 7 days ago - Pushed: 24 days ago - Stars: 16 - Forks: 11
eMetaboHUB/Forum-DiseasesChem
A Knowledge Graph from public databases and scientific literature to extract associations between chemicals and diseases.
Language: Python - Size: 30.8 MB - Last synced: 24 days ago - Pushed: 24 days ago - Stars: 14 - Forks: 6
CCMS-UCSD/GNPSDocumentation
Documentation for GNPS and related tools as written in mkdocs
Language: HTML - Size: 248 MB - Last synced: 27 days ago - Pushed: 28 days ago - Stars: 34 - Forks: 80
czbiohub-sf/Rapid-QC-MS
Realtime quality control for mass spectrometry data acquisition
Language: Python - Size: 4.4 MB - Last synced: 28 days ago - Pushed: 28 days ago - Stars: 10 - Forks: 2
yufree/pmd
Paired Mass Distance(PMD) analysis for GC/LC-MS based nontarget analysis
Language: R - Size: 78.1 MB - Last synced: 28 days ago - Pushed: 29 days ago - Stars: 9 - 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: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0
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: 30 days ago - Pushed: about 1 month ago - Stars: 44 - Forks: 14
rformassspectrometry/MetaboCoreUtils
Core utilities for metabolomics.
Language: R - Size: 13.4 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 7 - Forks: 6
OpenMS/OpenMS
The codebase of the OpenMS project
Language: C++ - Size: 609 MB - Last synced: about 1 month ago - Pushed: about 1 month 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: about 1 month ago - Pushed: about 1 month ago - Stars: 15 - Forks: 14
MoseleyBioinformaticsLab/mwtab
The mwtab package is a Python library that facilitates reading and writing files in mwTab format used by the Metabolomics Workbench for archival of Mass Spectrometry (MS) and Nuclear Magnetic Resonance (NMR) experimental data.
Language: Python - Size: 95.3 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 11 - Forks: 2
metaspace2020/metaspace
Cloud engine and platform for metabolite annotation for imaging mass spectrometry
Language: TypeScript - Size: 71.1 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 42 - Forks: 8
tnaake/MatrixQCvis
Language: R - Size: 4.47 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 5 - Forks: 1
NPLinker/nplinker
A python framework for data mining microbial natural products by integrating genomics and metabolomics data
Language: Jupyter Notebook - Size: 111 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 14 - Forks: 8
workflow4metabolomics/tools-metabolomics
Galaxy tools for metabolomics maintained by Workflow4Metabolomics
Language: R - Size: 1.31 GB - Last synced: 26 days ago - Pushed: about 1 month ago - Stars: 23 - Forks: 22
AndreHolzer/Metapolish
Metabolite Peak List Merge, Annotation & Polishing Tool: A user friendly, platform independent R tool to merge, annotate and polish metabolite-peak list data from LC-/GCMS runs
Language: R - Size: 11.8 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 2 - Forks: 1
p2m2/service-flask-thermorawfileparser-openms
A simple HTML interface for converting RAW format to MzML, MzXML, and MGF files.
Language: Python - Size: 10.7 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0
himelmallick/IntegratedLearner
Integrated Machine Learning for Multi-omics Classification and Prediction
Language: HTML - Size: 22.1 MB - Last synced: 7 days ago - Pushed: about 1 month ago - Stars: 11 - Forks: 4
ethanbass/chromatographR
Toolset for the reproducible analysis of chromatography data in R (HPLC-DAD/UV, GC-FID).
Language: R - Size: 107 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 12 - Forks: 2
ethanbass/mzinspectr
Load and analyze MS-DIAL alignment files in R for analysis of mass spectrometry data.
Language: R - Size: 160 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 2 - Forks: 0
cran-task-views/Omics
CRAN Task View: Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics
Size: 72.3 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 15 - Forks: 4
mapio/jp2rt
A Java and Python package to Predict Retention Times
Language: Java - Size: 286 KB - Last synced: 14 days ago - Pushed: about 1 month ago - Stars: 3 - Forks: 0
phenomecentre/nPYc-Toolbox
The nPYc-Toolbox defines objects for representing, and implements functions to manipulate and display, metabolic profiling datasets.
Language: Python - Size: 5.27 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 22 - Forks: 8
cwieder/py-ssPA
Single sample pathway analysis tools for omics data
Language: Jupyter Notebook - Size: 8.05 MB - Last synced: 10 days ago - Pushed: about 2 months ago - Stars: 9 - Forks: 4
biobakery/melonnpan
Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles
Language: R - Size: 3.81 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 33 - Forks: 8
AHuffmyer/EarlyLifeHistory_Energetics
Ontogenetic shifts in symbiotic and metabolic state in coral early life history
Language: HTML - Size: 407 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 5 - Forks: 1
ethanbass/chromConverter
Parsers for chromatography data in R (HPLC-DAD/UV, GC-FID, MS)
Language: R - Size: 6.74 MB - Last synced: 23 days ago - Pushed: about 2 months ago - Stars: 23 - Forks: 3
parthosen/parthosen.github.io
My personal website
Language: HTML - Size: 10.2 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 1
computational-metabolomics/struct
R/Bioconductor package - STRUCT: STatistics in R Using Class Templates
Language: R - Size: 1.19 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 5 - Forks: 0
egonw/metabolomics-practical
Size: 327 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 1 - Forks: 0
rformassspectrometry/book
R for Mass Spectrometry documentation
Language: TeX - Size: 16.3 MB - Last synced: 7 days ago - Pushed: about 2 months ago - Stars: 8 - Forks: 5
RECETOX/ei_spectra_predictions
This repository contains the workflow and supporting information for "Quantum chemistry based prediction of electron ionization mass spectra for environmental chemicals".
Language: Jupyter Notebook - Size: 117 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0
Philipbear/msbuddy
a python package for molecular formula analysis in MS-based small molecule studies
Language: Python - Size: 21.3 MB - Last synced: 26 days ago - Pushed: about 2 months ago - Stars: 15 - Forks: 2
yufree/xcmsrocker
Rocker image for metabolomics data analysis
Language: HTML - Size: 1000 KB - Last synced: 28 days ago - Pushed: 2 months ago - Stars: 12 - Forks: 3
rformassspectrometry/ProtGenerics
S4 generic functions for Bioconductor mass spectrometry infrastructure
Language: R - Size: 95.7 KB - Last synced: 7 days ago - Pushed: 2 months ago - Stars: 7 - Forks: 5
yufree/mzrtsim
Raw data and peaks list simulation for GC/LC-MS based data
Language: R - Size: 36.4 MB - Last synced: 28 days ago - Pushed: 2 months ago - Stars: 4 - Forks: 1
computational-metabolomics/pmp
R/Bioconductor package - Peak Matrix Processing and signal batch correction for metabolomics data sets
Language: R - Size: 3.7 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 1 - Forks: 1
SinaBerkGolech/Metabolomics_Seminar_Topic_10
Case studies of reproducibility in bioinformatics: Metabolomics
Language: Jupyter Notebook - Size: 130 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0
EBI-Metagenomics/holofood-database
HoloFood is a project investigating sustainable food production through hologenomics. This Django app is the data portal where samples and other datasets from the project are made publicly available.
Language: Python - Size: 20.3 MB - Last synced: about 1 month ago - Pushed: 2 months ago - Stars: 1 - Forks: 0
rformassspectrometry/CompoundDb
Creating and using (chemical) compound databases
Language: R - Size: 10.6 MB - Last synced: 7 days ago - Pushed: 3 months ago - Stars: 16 - Forks: 14
griquelme/tidyms
TidyMS: Tools for working with MS data in untargeted metabolomics
Language: Python - Size: 30.3 MB - Last synced: about 2 months ago - Pushed: 3 months ago - Stars: 49 - Forks: 11
aberHRML/metabolighteR
R Interface to the Metabolights REST API
Language: R - Size: 9.98 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 6 - Forks: 3
BiRG/pyopls
A Python 3 implementation of orthogonal projection to latent structures
Language: Python - Size: 1.69 MB - Last synced: 26 days ago - Pushed: 3 months ago - Stars: 55 - Forks: 16
tnaake/MsQuality
Language: R - Size: 19.2 MB - Last synced: 24 days ago - Pushed: 3 months ago - Stars: 7 - Forks: 0
mvisani/anticipated_lotus
Model performing predictions of occurence of metabolites in the LOTUS database using Subgraph Sketching.
Language: Python - Size: 105 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0
anitamnd/MetaboLink
Repository for metabolomics and lipidomics data processing app.
Language: R - Size: 2.1 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 1