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

opencobra/cobratoolbox

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

Language: MATLAB - Size: 1.02 GB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 237 - Forks: 303

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

sneumann/xcms

This is the git repository matching the Bioconductor package xcms: LC/MS and GC/MS Data Analysis

Language: R - Size: 121 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 157 - Forks: 78

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

ElucidataInc/ElMaven

LC-MS data processing tool for large-scale metabolomics experiments.

Language: C++ - Size: 643 MB - Last synced: 7 months ago - Pushed: almost 2 years ago - Stars: 84 - Forks: 48

CCMS-UCSD/GNPS_Workflows

Public Workflows at GNPS

Language: HTML - Size: 266 MB - Last synced: 7 months ago - Pushed: 9 months ago - Stars: 41 - Forks: 42

boecker-lab/sirius-libs

sirius-libs - Metabolomics mass spectrometry framework for molecular formula identification of small molecules written in Java

Language: Java - Size: 48.1 MB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 46 - Forks: 27

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

rformassspectrometry/Spectra

Low level infrastructure to handle MS spectra

Language: R - Size: 19.2 MB - Last synced: about 5 hours ago - Pushed: about 5 hours ago - Stars: 31 - Forks: 23

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

MolecularCartography/ili

Web-based software for visualization of molecular maps in 2D and 3D

Language: JavaScript - Size: 141 MB - Last synced: 7 months ago - Pushed: 10 months ago - Stars: 25 - Forks: 21

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

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

wfondrie/depthcharge

A deep learning toolkit for mass spectrometry

Language: Python - Size: 1.29 MB - Last synced: 5 days ago - Pushed: 6 days ago - Stars: 51 - Forks: 16

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

biocore/q2-qemistree

Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".

Language: Python - Size: 87.3 MB - Last synced: 7 months ago - Pushed: about 1 year ago - Stars: 24 - Forks: 16

tubanlee/MM

Infer metabolic directions from moment differences of mass-weighted intensity distributions

Language: R - Size: 4.17 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 186 - Forks: 14

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

PaoloBnn/Retip

Retip - Retention Time prediction for metabolomics

Language: R - Size: 61.3 MB - Last synced: 7 months ago - Pushed: about 2 years ago - Stars: 28 - Forks: 14

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

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: 29 days ago - Pushed: about 1 month ago - Stars: 44 - Forks: 14

wenbostar/metaX

metaX: a flexible and comprehensive software for processing omics data.

Language: R - Size: 51.2 MB - Last synced: 9 months ago - Pushed: 11 months ago - Stars: 14 - Forks: 12

barupal/ChemRICH

Chemical Similarity Enrichment analysis of metabolomics datasets

Language: R - Size: 158 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 22 - Forks: 12

MolecularCartography/Optimus

Workflow for LC-MS feature analysis and spatial mapping

Language: Python - Size: 118 MB - Last synced: about 1 year ago - Pushed: almost 6 years ago - Stars: 17 - Forks: 12

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

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

rformassspectrometry/metaRbolomics-book

The MetaRbolomics book. A review of R packages in BioC, CRAN, gitlab and github.

Language: TeX - Size: 82.7 MB - Last synced: 7 days ago - Pushed: about 3 years ago - Stars: 32 - Forks: 10

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

computational-metabolomics/dimspy

Python package for processing direct-infusion mass spectrometry-based metabolomics and lipidomics data

Language: Python - Size: 107 MB - Last synced: 24 days ago - Pushed: 10 months ago - Stars: 18 - Forks: 10

secimTools/SECIMTools

A set of metabolomics tools for use in Galaxy

Language: Jupyter Notebook - Size: 516 MB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 11 - Forks: 9

rformassspectrometry/MetaboAnnotation

High level functionality to support and simplify metabolomics data annotation.

Language: R - Size: 12.4 MB - Last synced: about 17 hours ago - Pushed: 1 day ago - Stars: 11 - Forks: 9

ablab/npdtools

Natural Product Discovery tools -- a toolkit containing various pipelines for in silico analysis of natural product mass spectrometry data

Size: 1.1 MB - Last synced: 7 days ago - Pushed: over 1 year ago - Stars: 22 - Forks: 9

Russel88/DAtest

Compare different differential abundance and expression methods

Language: R - Size: 1.54 MB - Last synced: 7 months ago - Pushed: about 2 years ago - Stars: 46 - Forks: 9

aberHRML/classyfireR

R Interface to the ClassyFire REST API

Language: R - Size: 1.42 MB - Last synced: 5 months ago - Pushed: over 1 year ago - Stars: 8 - Forks: 9

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

pyQms/pyqms

pyQms, generalized, fast and accurate mass spectrometry data quantification

Language: Python - Size: 1.93 MB - Last synced: 18 days ago - Pushed: 5 months ago - Stars: 28 - Forks: 9

DTUComputeStatisticsAndDataAnalysis/MBPLS

(Multiblock) Partial Least Squares Regression for Python

Language: Python - Size: 16.6 MB - Last synced: 5 days ago - Pushed: over 4 years ago - Stars: 28 - Forks: 8

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

MetaSys-LISBP/IsoCor

IsoCor: Isotope Correction for mass spectrometry labeling experiments

Language: Python - Size: 2.39 MB - Last synced: 28 days ago - Pushed: 6 months ago - Stars: 24 - Forks: 8

glasgowcompbio/ms2ldaviz

Substructural discovery in untargeted metabolomics data using LDA topic modelling.

Language: Jupyter Notebook - Size: 43 MB - Last synced: about 1 month ago - Pushed: 6 months ago - Stars: 11 - Forks: 8

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

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

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

Philipbear/BUDDY_Metabolomics

Molecular formula discovery via bottom-up MS/MS interrogation

Language: C# - Size: 149 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 11 - Forks: 8

microbiomedata/nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model

Language: Python - Size: 115 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 27 - Forks: 8

RogerGinBer/RHermes

RHermes is a semi-targeted metabolomics package to deeply characterize biological and environmental samples.

Language: R - Size: 12.8 MB - Last synced: 7 months ago - Pushed: 9 months ago - Stars: 23 - Forks: 7

glasgowcompbio/vimms

A programmable and modular LC/MS simulator in Python

Language: Python - Size: 235 MB - Last synced: 23 days ago - Pushed: 23 days ago - Stars: 17 - Forks: 7

stanstrup/commonMZ

A collection of common mz values found in mass spectrometry.

Language: R - Size: 208 KB - Last synced: 9 months ago - Pushed: almost 2 years ago - Stars: 16 - Forks: 7

IngallsLabUW/Targeted_Pipeline

Targeted pipeline to quantify metabolomics datasets produced by QExactive and Triple Quadrupole Mass Specs.

Language: R - Size: 32 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 7

hcji/KPIC2

KPIC2: An Effective Framework for Mass Spectrometry-Based Metabolomics Using Pure Ion Chromatograms

Language: R - Size: 5.26 MB - Last synced: 7 months ago - Pushed: about 1 year ago - Stars: 7 - Forks: 7

13479776/statTarget

Statistical Analysis of Molecular Profile https://stattarget.github.io

Language: R - Size: 5.48 MB - Last synced: 7 months ago - Pushed: almost 4 years ago - Stars: 4 - Forks: 6

yufree/enviGCMS

GC/LC-MS data analysis for environmental science

Language: R - Size: 175 MB - Last synced: 19 days ago - Pushed: 8 months ago - Stars: 15 - Forks: 6

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

stanstrup/PredRet

Shiny app for retention time prediction

Language: JavaScript - Size: 18.4 MB - Last synced: 7 months ago - Pushed: over 4 years ago - Stars: 8 - Forks: 6

Metaboverse/Metaboverse

Visualization and analysis platform for metabolic data and network pattern recognition

Language: JavaScript - Size: 511 MB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 38 - Forks: 6

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

computational-metabolomics/mspurity-galaxy

Galaxy tools for msPurity package: includes precursor ion purity calculations and spectral matching

Language: R - Size: 73.4 MB - Last synced: 9 months ago - Pushed: over 2 years ago - Stars: 1 - Forks: 6

mjhelf/Metaboseek

Interactive software to analyze and browse mass spectrometry data

Language: R - Size: 176 MB - Last synced: 7 months ago - Pushed: 9 months ago - Stars: 18 - Forks: 6

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

CCMS-UCSD/GNPS_TrainingTutorialModules

Standard Tutorial Modules for GNPS Workshops

Size: 233 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 3 - Forks: 6

workflow4metabolomics/w4m-docker

Docker for Workflow4Metabolomics Galaxy platform.

Language: Dockerfile - Size: 8.98 MB - Last synced: 26 days ago - Pushed: almost 5 years ago - Stars: 5 - Forks: 6

jcapelladesto/geoRge

geoRge: a computational tool for stable isotope labelling detection in LC/MS-based untargeted metabolomics

Language: R - Size: 20.2 MB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 7 - Forks: 6

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

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

eMetaboHUB/MS-CleanR

Language: R - Size: 37.9 MB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 21 - Forks: 5

zmzhang/pymass

Package for analyzing MS with Python

Language: C - Size: 133 KB - Last synced: 9 months ago - Pushed: over 6 years ago - Stars: 9 - Forks: 5

bebop/ark

Go REST API to replace Genbank, Uniprot, Rhea, and CHEMBL

Language: Go - Size: 17 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 19 - Forks: 5

pcastellanoescuder/POMAShiny

:apple: Web-based User-friendly Workflow for Metabolomics and Proteomics Data Analysis

Language: R - Size: 21.4 MB - Last synced: 4 days ago - Pushed: about 1 year ago - Stars: 16 - Forks: 5

metaspace2020/sm-engine 📦

Engine for metabolite annotation for imaging mass spectrometry

Language: Python - Size: 45 MB - Last synced: 7 months ago - Pushed: almost 6 years ago - Stars: 6 - Forks: 5

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

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

computational-metabolomics/beamspy

BEAMSpy - Birmingham mEtabolite Annotation for Mass Spectrometry (Python Package)

Language: Python - Size: 76.7 MB - Last synced: 6 days ago - Pushed: about 1 year ago - Stars: 15 - Forks: 5

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

MoTrPAC/MotrpacBicQC

R package for the MoTrPAC community

Language: R - Size: 3.6 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 8 - Forks: 4

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

glasgowcompbio/pyMultiOmics

Python toolbox for multi-omics data mapping and analysis

Language: Jupyter Notebook - Size: 45.9 MB - Last synced: 21 days ago - Pushed: about 1 year ago - Stars: 15 - Forks: 4

pcastellanoescuder/FoodBiomarkerOntology

:rocket: Food-Biomarker Ontology defines the relationships between foods and their associated metabolites (biomarkers) through a formal ontology

Language: Python - Size: 6.75 MB - Last synced: 4 days ago - Pushed: about 2 years ago - Stars: 16 - Forks: 4

tnaake/MetNet

GitHub repository for MetNet. The development version in Bioconductor can be found at:

Language: R - Size: 23.7 MB - Last synced: 5 months ago - Pushed: about 1 year ago - Stars: 1 - Forks: 4

respiratory-immunology-lab/metabolome-lipidome-MSDIAL

Guide to processing raw LCMS metabolomic and lipidomic data using MS-DIAL, followed by data pre-processing and secondary annotation (of metabolites) in R.

Language: R - Size: 37.4 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 9 - Forks: 4

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

workflow4metabolomics/workflow4metabolomics

Workflow4Metabolomics meta repository

Language: HTML - Size: 12.5 MB - Last synced: 26 days ago - Pushed: over 2 years ago - Stars: 10 - Forks: 4

barupal/metamapp

R codes for creating metamapp graphs and files

Language: JavaScript - Size: 2.41 MB - Last synced: 7 months ago - Pushed: almost 2 years ago - Stars: 7 - Forks: 4

computational-metabolomics/dimspy-galaxy

Galaxy tools for Python package DIMSpy: data processing of Direct-Infusion Mass Spectrometry-based metabolomics and lipidomics data

Size: 14.8 MB - Last synced: about 1 month ago - Pushed: about 3 years ago - Stars: 4 - Forks: 4

CHKim5/LMSstat

Package for automation of statistics that are widely used in metabolomics.

Language: R - Size: 392 KB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 3 - Forks: 4

computational-metabolomics/structToolbox

R/Bioconductor package - STRUCT (STatistics in R Using Class Templates) Toolbox

Language: R - Size: 24.7 MB - Last synced: 13 days ago - Pushed: 3 months ago - Stars: 8 - Forks: 4

barupal/exposome

The Blood Exposome Database

Language: R - Size: 144 KB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 3 - Forks: 4

bridgedb/create-bridgedb-metabolites Fork of egonw/create-bridgedb-metabolites

Create BridgeDb identity mapping files from HMDB, ChEBI, and Wikidata

Language: Groovy - Size: 4.06 MB - Last synced: about 1 month ago - Pushed: about 1 year ago - Stars: 4 - Forks: 4

samhinshaw/metabridge_shiny

🕸 Network-based multi-omic integration of metabolomics data.

Language: R - Size: 79 MB - Last synced: 7 months ago - Pushed: about 1 year ago - Stars: 6 - Forks: 4

yufree/xcmsrocker

Rocker image for metabolomics data analysis

Language: HTML - Size: 1000 KB - Last synced: 27 days ago - Pushed: 2 months ago - Stars: 12 - Forks: 3

metgem/metgem

Calculation and visualization of molecular networks based on t-SNE algorithm

Language: Python - Size: 16.9 MB - Last synced: about 7 hours ago - Pushed: about 8 hours ago - Stars: 28 - Forks: 3

i6092467/NNGC-SLIMMBA

Nonlinear Granger causality inference with neural networks for high-resolution mass spectrometry

Language: Python - Size: 5.82 MB - Last synced: about 1 month ago - Pushed: over 2 years ago - Stars: 13 - Forks: 3

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

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

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: 23 days ago - Stars: 19 - Forks: 3

novak-jiri/cyclobranch

A tool for mass spectrometry data analysis.

Language: C++ - Size: 5.27 MB - Last synced: 7 months ago - Pushed: 9 months ago - Stars: 7 - Forks: 3

okadalabipr/ccle_extractor

Python script for extracting dataset from CCLE (Cancer Cell Line Encyclopedia)

Language: Python - Size: 41 KB - Last synced: about 1 year ago - Pushed: almost 3 years ago - Stars: 6 - Forks: 3

hcji/TarMet

An R package and Shiny App for MS-Based Targeted Metabolic Analyses

Language: R - Size: 33.6 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 7 - Forks: 3

jorainer/MetaboAnnotationTutorials

Examples and tutorials for the MetaboAnnotation, MetaboCoreUtils and CompoundDb R packages

Language: TeX - Size: 14 MB - Last synced: 1 day ago - Pushed: 5 months ago - Stars: 7 - Forks: 3

RECETOX/workflow-reports

Size: 8.79 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 3