metabolomics

opencobra/cobratoolbox

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

sneumann/xcms

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

matchms/matchms

Python library for processing (tandem) mass spectrometry data and for computing spectral similarities.

ElucidataInc/ElMaven

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

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)

tubanlee/MM

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

pnnl/isicle

In silico chemical library engine for high-accuracy chemical property prediction

BiRG/pyopls

A Python 3 implementation of orthogonal projection to latent structures

wfondrie/depthcharge

A deep learning toolkit for mass spectrometry

CCMS-UCSD/GNPS_Workflows

Public Workflows at GNPS

sirius-ms/sirius-libs

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

griquelme/tidyms

TidyMS: Tools for working with MS data in untargeted metabolomics

EMSL-Computing/CoreMS

CoreMS is a comprehensive mass spectrometry software framework

Russel88/DAtest

Compare different differential abundance and expression methods

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.

metaspace2020/metaspace

Cloud engine and platform for metabolite annotation for imaging mass spectrometry

Metaboverse/Metaboverse

Visualization and analysis platform for metabolic data and network pattern recognition

CCMS-UCSD/GNPSDocumentation

Documentation for GNPS and related tools as written in mkdocs

biobakery/melonnpan

Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles

rformassspectrometry/Spectra

Low level infrastructure to handle MS spectra

rformassspectrometry/metaRbolomics-book

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

biocore/q2-qemistree

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

oloBion/Retip

Retip - Retention Time prediction for metabolomics

DTUComputeStatisticsAndDataAnalysis/MBPLS

(Multiblock) Partial Least Squares Regression for Python

metgem/metgem

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

mmzdouc/FERMO

Dashboard for analysis of liquid chromatography (tandem) mass spectrometry data.

pyQms/pyqms

pyQms, generalized, fast and accurate mass spectrometry data quantification

MolecularCartography/ili

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

barupal/ChemRICH

Chemical Similarity Enrichment analysis of metabolomics datasets

microbiomedata/nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model

eMetaboHUB/MS-CleanR

RogerGinBer/RHermes

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

ethanbass/chromConverter

Parsers for chromatography data in R (HPLC-DAD/UV, GC-FID, MS)

MetaSys-LISBP/IsoCor

IsoCor: Isotope Correction for mass spectrometry labeling experiments

workflow4metabolomics/tools-metabolomics

Galaxy tools for metabolomics maintained by Workflow4Metabolomics