metabolomics

There are 22 repositories under metabolomics topic.

OpenMS / OpenMS
The codebase of the OpenMS project
openms c-plus-plus ms-data mass-spectrometry linux macos windows proteomics analyses algorithms metabolomics 3-clause-bsd hacktoberfest
Language:C++ 456
opencobra / cobratoolbox
The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
cobra-toolbox reconstruction tutorial metabolic-models metabolic-reconstruction metabolic-engineering gap-filling strain-engineering omics-data-integration metabolomics transcriptomics cobra constraint-based-modeling human-metabolism microbiome-analysis
Language:MATLAB 237
sneumann / xcms
This is the git repository matching the Bioconductor package xcms: LC/MS and GC/MS Data Analysis
bioconductor metabolomics mass-spectrometry peak-detection feature-detection r
Language:R 171
matchms / matchms
Python library for processing (tandem) mass spectrometry data and for computing spectral similarities.
analysis fuzzy-matching fuzzy-search mass-spectrometry metabolomics python3 similarity-measures
Language:Python 163
ElucidataInc / ElMaven
LC-MS data processing tool for large-scale metabolomics experiments.
metabolomics mass-spectrometry lc-ms qt c-plus-plus lc-msms
Language:C++ 85
boecker-lab / 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)
denovo metabolomics mass-spectrometry java science cheminformatics bioinformatics molecular-structures molecular-formulas ms-spectra ms-data structure-elucidation fragmentation-trees sirius csi-fingerid fingerid isotope-pattern mass-spectra
Language:Java 75
tubanlee / MM
Infer metabolic directions from moment differences of mass-weighted intensity distributions
annotations mass-spectra mass-spectrometry mass-spectrometry-data mass-spectrum metabolic-flux-analysis metabolic-models metabolic-network metabolic-networks metabolic-pathways metabolic-engineering metabolomics moment moments
Language:R 59
pnnl / isicle
In silico chemical library engine for high-accuracy chemical property prediction
metabolomics standards-free collision-cross-section high-performance-computing computational-chemistry density-functional-theory molecular-dynamics ion-mobility quantum-chemistry chemical-shifts
Language:Python 57
BiRG / pyopls
A Python 3 implementation of orthogonal projection to latent structures
chemometrics feature-selection metabolomics orthogonal-signal-correction partial-least-squares-regression
Language:Python 55
depthcharge
wfondrie / depthcharge
A deep learning toolkit for mass spectrometry
deep-learning framework mass-spectrometry metabolomics proteomics pytorch
Language:Python 51
boecker-lab / sirius-libs
sirius-libs - Metabolomics mass spectrometry framework for molecular formula identification of small molecules written in Java
java-library denovo metabolomics cheminformatics bioinformatics mass-spectrometry molecular-formulas ms-spectra ms-data scientific-computing
Language:Java 50
griquelme / tidyms
TidyMS: Tools for working with MS data in untargeted metabolomics
mass-spectrometry metabolomics
Language:Python 50
Russel88 / DAtest
Compare different differential abundance and expression methods
microbiome rnaseq relative-abundances compare-methods differential-abundance-methods otu marker-gene-analysis 16s proteomics metabolomics metagenomics differential-expression auc false-positive-control
Language:R 48
CCMS-UCSD / GNPS_Workflows
Public Workflows at GNPS
gnps mass-spectrometry molecularnetworking metabolomics naturalproducts untargeted
Language:HTML 46
EMSL-Computing / CoreMS
CoreMS is a comprehensive mass spectrometry software framework
complex-mixture data-analysis dissolved-organic-matter mass-spectrometry metabolomics metabolomics-pipeline molecular-database molecular-formulae-assignment molecular-search natural-organic-matter soil-organic-matter
Language:Python 46
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.
visualbasic metadna lc-ms gc-ms kegg metabolomics r-sharp ms-imaging gcxgc maldi chemoinformatics single-cell single-cell-metabolism mass-spectrometry mzkit raman-spectroscopy ms-dial lipidomics
Language:Visual Basic .NET 44
metaspace2020 / metaspace
Cloud engine and platform for metabolite annotation for imaging mass spectrometry
bioinformatics cloud metabolomics
Language:TypeScript 42
Metaboverse / Metaboverse
Visualization and analysis platform for metabolic data and network pattern recognition
chemical d3 metabolism metabolomics network networkx pattern-recognition proteomics reaction sequencing
Language:JavaScript 38
CCMS-UCSD / GNPSDocumentation
Documentation for GNPS and related tools as written in mkdocs
gnps massspectrometery metabolomics naturalproducts
Language:HTML 34
biobakery / melonnpan
Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles
microbiome metabolomics metagenomics machine-learning public tools biobakery bioconductor metabolite-prediction multi-omics metabolite-compounds microbial-communities
Language:R 33
rformassspectrometry / metaRbolomics-book
The MetaRbolomics book. A review of R packages in BioC, CRAN, gitlab and github.
r metabolomics multivariate-statistics lc-ms lc-msms nmr nmr-spectroscopy nmr-data lcms metabonomics rstats
Language:TeX 32
rformassspectrometry / Spectra
Low level infrastructure to handle MS spectra
rstats mass-spectrometry proteomics metabolomics bioconductor
Language:R 31
biocore / q2-qemistree
Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".
metabolomics cheminformatics microbiome fragmentation-trees phylogenetics
Language:Python 30
Retip
PaoloBnn / Retip
Retip - Retention Time prediction for metabolomics
lcms metabolomics retention-time
Language:R 30
DTUComputeStatisticsAndDataAnalysis / MBPLS
(Multiblock) Partial Least Squares Regression for Python
chemometrics metabolomics data-science pattern-recognition multivariate-statistics subspace-learning supervised-learning data-fusion data-integration multivariate-analysis machine-learning bioinformatics
Language:Python 28
metgem / metgem
Calculation and visualization of molecular networks based on t-SNE algorithm
chemistry chemoinformatics mass-spectrometry cosine-similarity networking graph network metabolomics
Language:Python 28
pyQms / pyqms
pyQms, generalized, fast and accurate mass spectrometry data quantification
mass-spectrometry proteomics metabolomics lipidomics computational-biology ms-data
Language:Python 28
MolecularCartography / ili
Web-based software for visualization of molecular maps in 2D and 3D
3d-map bootstrap3 cartography chrome-extension javascript mass-spectrometry metabolomics metagenomics spatial-data threejs visualization
Language:JavaScript 27
barupal / ChemRICH
Chemical Similarity Enrichment analysis of metabolomics datasets
bioinformatics enrichment metabolomics opencpu
Language:R 26
microbiomedata / nmdc-schema
National Microbiome Data Collaborative (NMDC) unified data model
ecoinformatics fair-data genomics linkml metabolomics metadata microbiome microbiomedata mixs nmdc proteomics samples schema standards transcriptomics
Language:Python 26
mmzdouc / FERMO
Dashboard for analysis of liquid chromatography (tandem) mass spectrometry data.
biological-data-analysis exposomics mass-spectrometry metabolomics python3
Language:Python 26
MS-CleanR
eMetaboHUB / MS-CleanR
annotation lc-ms-data metabolomics
Language:R 25
RogerGinBer / RHermes
RHermes is a semi-targeted metabolomics package to deeply characterize biological and environmental samples.
r metabolomics gui metabolite-identification
Language:R 25
MetaSys-LISBP / IsoCor
IsoCor: Isotope Correction for mass spectrometry labeling experiments
ms-data isotope-labeling-experiments isotope mass-spectrometry metabolomics isotope-correction fluxomics 13c-mfa metabolic-flux-analysis correction-natural-abundance isotopologue-distribution isotopic-inchi
Language:Python 24
chromConverter
ethanbass / chromConverter
Parsers for chromatography data in R (HPLC-DAD/UV, GC-FID, MS)
chromatography r-package hplc hplc-dad hplc-uv cheminformatics metabolomics metabolomics-data open-science gc-fid r rstats open-data fair-data
Language:R 23
phenomecentre / nPYc-Toolbox
The nPYc-Toolbox defines objects for representing, and implements functions to manipulate and display, metabolic profiling datasets.
quality-control metabolomics metabolic-phenotyping
Language:Python 23