idslme/IDSL.UFA

United Formula Annotation (UFA) for LC-HRMS data

Language: R - Size: 3.17 MB - Last synced: 26 days ago - Pushed: 12 months ago - Stars: 7 - Forks: 1

tnaake/MsQuality

Language: R - Size: 19.2 MB - Last synced: 24 days ago - Pushed: 3 months ago - Stars: 7 - Forks: 0

yufree/enet

network analysis for exposure study

Language: R - Size: 3.53 MB - Last synced: 27 days ago - Pushed: about 2 years ago - Stars: 2 - Forks: 0

rformassspectrometry/SpectraVis

Visualising Spectra Data

Language: R - Size: 1.12 MB - Last synced: 7 days ago - Pushed: about 2 years ago - Stars: 4 - 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

MetaSys-LISBP/IsoSolve Fork of sgsokol/IsoSolve

Integration of isotopic measurements

Language: Python - Size: 1 MB - Last synced: 29 days ago - Pushed: about 3 years ago - Stars: 4 - Forks: 1

MetaSys-LISBP/IsoSolve_notebook

Showcase IsoSolve

Language: HTML - Size: 11.1 MB - Last synced: 29 days ago - Pushed: about 3 years ago - Stars: 3 - Forks: 2

YonghuiDong/MSbox

Tools for Metabolomics and mass Spectrometry users

Language: R - Size: 7.97 MB - Last synced: 26 days ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

MetaSys-LISBP/zerter

Extract signals from J-resolved NMR spectra (Cox et al., 2020)

Language: Python - Size: 17.6 KB - Last synced: 29 days ago - Pushed: over 3 years ago - Stars: 1 - Forks: 0

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

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

MetaSys-LISBP/IsoQ

Simultaneous measurement of absolute metabolite concentration and isotope incorporation by mass spectrometry

Language: Python - Size: 2.22 MB - Last synced: 29 days ago - Pushed: over 4 years ago - Stars: 2 - Forks: 1

LewisResearchGroup/ms-mint

Targeted metabolomics with Python

Language: Jupyter Notebook - Size: 418 MB - Last synced: 19 days ago - Pushed: 8 months ago - Stars: 19 - Forks: 3

cheminfo/COMPASS

Strategy for improved characterisation of human metabolic phenotypes using a COmbined Multiblock Principal components Analysis with Statistical Spectroscopy (COMPASS)

Language: R - Size: 14.5 MB - Last synced: about 1 month ago - Pushed: almost 4 years ago - Stars: 3 - Forks: 1

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

bihealth/metaquac 📦

Metabolomics Targeted Quality Control

Language: R - Size: 1.96 MB - Last synced: about 1 month ago - Pushed: almost 3 years ago - Stars: 8 - Forks: 1

rformassspectrometry/MsBackendHmdb

Mass spectrometry data backend (MsBackend) for Spectra supporting import and handling of MS/MS spectra from the Human Metabolome Database (HMDB).

Language: R - Size: 95.7 KB - Last synced: 7 days ago - Pushed: about 2 years ago - Stars: 1 - Forks: 0

BiRG/pyopls

A Python 3 implementation of orthogonal projection to latent structures

Language: Python - Size: 1.69 MB - Last synced: 25 days ago - Pushed: 3 months ago - Stars: 55 - Forks: 16

kmcluskey/FlyMet

A multi-omics web app for Drosophila tissues

Language: Python - Size: 25.9 MB - Last synced: about 1 month ago - Pushed: about 1 year ago - Stars: 3 - Forks: 0

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

yufree/mdaw

Metabolomics Data Analysis Workshop slides

Language: JavaScript - Size: 898 KB - Last synced: 27 days ago - Pushed: over 4 years ago - Stars: 5 - Forks: 0

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

yufree/metaRSS

RSS for metabolomics research

Language: HTML - Size: 1000 KB - Last synced: 27 days ago - Pushed: about 1 year ago - Stars: 1 - Forks: 0

wikipathways/summit2018

WikiPathways Summit Planning

Size: 2.93 KB - Last synced: 7 days ago - Pushed: over 5 years ago - Stars: 2 - Forks: 0

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

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

yufree/mzrtsim

Raw data and peaks list simulation for GC/LC-MS based data

Language: R - Size: 36.4 MB - Last synced: 27 days ago - Pushed: 2 months ago - Stars: 4 - Forks: 1

MoseleyBioinformaticsLab/isoenum

Isotopic (iso) enumerator (enum) - enumerates isotopically resolved InChI (International Chemical Identifier) for metabolites.

Language: Python - Size: 183 KB - Last synced: about 1 month ago - Pushed: almost 5 years ago - Stars: 4 - Forks: 0

ccdmb/BioDendro

A package to cluster and visualise MS/MS spectral data

Language: Jupyter Notebook - Size: 10.1 MB - Last synced: 25 days ago - Pushed: about 3 years ago - Stars: 10 - Forks: 0

computational-metabolomics/beamspy-galaxy

Galaxy tools for BEAMSpy: Birmingham mEtabolite Annotation for Mass SpectroMetry (Python Package)

Language: Python - Size: 1.1 MB - Last synced: about 1 month ago - Pushed: about 2 years ago - Stars: 2 - Forks: 2

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

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

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

ISA-tools/MSIO

Metabolomics Standards Initiative Ontology

Language: Java - Size: 28.1 MB - Last synced: about 1 month ago - Pushed: 10 months ago - Stars: 5 - Forks: 2

sivx76/metabolomics

Work from the Dorrestein Laboratory for processing complex mass spectrometry data.

Language: Python - Size: 14.6 KB - Last synced: 15 days ago - Pushed: over 6 years ago - Stars: 1 - Forks: 0

AberystwythSystemsBiology/dimedbpy

Python wrapper for the DIMEdb REST API.

Language: Python - Size: 43.9 KB - Last synced: 14 days ago - Pushed: almost 2 years ago - Stars: 5 - Forks: 0

AberystwythSystemsBiology/DIMEpy 📦

Python package for the high-throughput nontargeted metabolite fingerprinting of nominal mass direct injection mass spectrometry directly from mzML files.

Language: Python - Size: 1.67 MB - Last synced: 29 days ago - Pushed: over 2 years ago - Stars: 9 - Forks: 3

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

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

AberystwythSystemsBiology/DIMEdb

DIMEdb: Metabolite identification web service.

Language: HTML - Size: 3.75 MB - Last synced: 29 days ago - Pushed: about 2 years ago - Stars: 3 - Forks: 0

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

workflow4metabolomics/camera.archive 📦

🚫 move to https://github.com/workflow4metabolomics/tools-metabolomics

Language: R - Size: 94.7 MB - Last synced: 26 days ago - Pushed: almost 5 years ago - Stars: 1 - Forks: 1

tyo-nu/MINE-app

Web application for the MINE databases

Language: CSS - Size: 9.84 MB - Last synced: about 2 months ago - Pushed: almost 2 years ago - Stars: 4 - Forks: 1

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

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

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

EBI-Metabolights/Metabolights-Labs

Online staging area to facilitate cloud based data analysis, re-analysis and submissions

Language: JavaScript - Size: 784 KB - Last synced: about 1 month ago - Pushed: over 5 years ago - Stars: 4 - Forks: 0

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

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/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

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

rformassspectrometry/MsDataHub

Mass Spectrometry Data on ExperimentHub

Language: R - Size: 196 KB - Last synced: 6 months ago - Pushed: 11 months ago - Stars: 1 - 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

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

jmbadia/MS2ID

High-throughput MS/MS annotation with a in-house database

Language: R - Size: 20.2 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 3 - Forks: 1

Waddlessss/metabengine

Ion-identity-informed metabolomics data processing

Language: Python - Size: 1.91 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 1 - Forks: 1

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

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

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

idslme/IDSL_MINT

A Deep Learning Framework to Interpret Raw Mass Spectrometry (m/z) Data

Language: Python - Size: 972 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 4 - Forks: 1

idslme/CCDB

Chemical Correlation Database (CCDB)

Language: R - Size: 7.82 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 3 - Forks: 0

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

areias03/tmCOM

GitHub repository to support the development of the thesis "Development of microbial community simulation methods to characterize and analyze the effects of metal concentrations on pathogen silencing/promotion".

Language: Jupyter Notebook - Size: 107 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

OmicsSuite/OmicsSuite.github.io

OmicsSuite website for releasing new version.

Language: HTML - Size: 14.8 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 15 - Forks: 1

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

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

tnaake/MsQualityUtils

Language: R - Size: 1.63 MB - Last synced: 5 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

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

PiotrTymoszuk/biggrExtra

metabolic pathway modeling based on gene expression

Language: R - Size: 9.34 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0

tomszar/ADNI_project

Sex difference analysis on AD metabolome

Language: Python - Size: 494 KB - Last synced: 5 months ago - Pushed: about 2 years ago - Stars: 0 - Forks: 1

AlinaPeluso/PhenoMeNal

R package for the estimation of metabolome-wide significance level and corresponding effective number of tests

Language: R - Size: 7.45 MB - Last synced: 6 months ago - Pushed: about 4 years ago - Stars: 1 - Forks: 0

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

pietrofranceschi/Metabolomics_lectures

Language: HTML - Size: 106 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 5 - Forks: 3

tnaake/MetCirc

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

Language: R - Size: 8.77 MB - Last synced: 5 months ago - Pushed: about 1 year ago - Stars: 4 - Forks: 2

mandelbrot-project/pf_1600_datanote

This repository gathers scripts used for the paper "Open and re-usable annotated mass spectrometry dataset of a chemodiverse collection of 1,600 plant extracts."

Language: Python - Size: 137 MB - Last synced: 4 months ago - Pushed: 10 months ago - Stars: 6 - Forks: 2

austinchia/Feno_Mouse

Data cleaning and preparation of fenofibrate MS data

Language: R - Size: 5.86 KB - Last synced: 6 months ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

Electrum-app/Electrum

Visualization platform for exploring MIDAS protein-small molecule interaction data

Language: Jupyter Notebook - Size: 59.1 MB - Last synced: about 2 months ago - Pushed: 8 months ago - Stars: 1 - Forks: 0

jwist/hastaLaVista

R package that provide interactive graphical interface for metabolic profiling

Language: JavaScript - Size: 98.5 MB - Last synced: 2 months ago - Pushed: 4 months ago - Stars: 5 - Forks: 2

klevdiamanti/MS_targeted

MS_targeted is an open-source command-line pipeline for statistical analysis of mass spectrometry metabolomics data.

Language: C# - Size: 30.1 MB - Last synced: 6 months ago - Pushed: over 4 years ago - Stars: 4 - Forks: 0

klevdiamanti/metabolomicsDB

metabolomicsDB is a collection of three open-source command-line tools and an API. The tools create a meta-database of HMDB and ChEBI, while the API allows others to read the meta-database and use it on their own projects.

Language: C# - Size: 126 MB - Last synced: 6 months ago - Pushed: over 1 year ago - Stars: 4 - Forks: 0

plyush1993/DReamGAMM

DReamGAMM: Dose-Response EnhAnced Modeling by Generalized Additive Mixed Model

Language: R - Size: 2.74 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 1 - Forks: 0

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

pwendering/model-prm

Constraint-based modeling of photorespiratory mutants using metabolomics in TMFA

Language: MATLAB - Size: 204 MB - Last synced: 4 months ago - Pushed: 6 months ago - Stars: 1 - Forks: 0

bmrb-io/smolscripts

small molecule processing scripts

Language: Python - Size: 552 KB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 0 - Forks: 0

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

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

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

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

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

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

mbongaerts/Metchalizer

Language: Jupyter Notebook - Size: 156 MB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 2 - Forks: 1

lifs-tools/rmzTab-m

The R-language bindings for mzTab-M

Language: R - Size: 2.04 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 2 - Forks: 1

jkdel/IDQprocessor

Set of functions to work with data exported from MetIDQ

Language: R - Size: 91.8 KB - Last synced: 7 months ago - Pushed: about 4 years ago - Stars: 0 - Forks: 0

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

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/MAPD

Mass Spectrometry Assisted Peak Detection Algorithm of Pure Ion Chromatograms from LC-MS

Language: R - Size: 2.08 MB - Last synced: 7 months ago - Pushed: almost 6 years ago - Stars: 1 - Forks: 2

GarrettLab-UF/LipidMatch-Normalizer

Quantify lipids using a feature table and internal standards table

Language: R - Size: 72.3 KB - Last synced: 7 months ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 2

fikipollo/stategraems

STATegra EMS: an Experiment Management System for complex next-generation omics experiments

Language: Java - Size: 190 MB - Last synced: 7 months ago - Pushed: over 6 years ago - Stars: 1 - Forks: 1

EuracBiomedicalResearch/biocResort

Resorting a Biocrates injection list for Sciex machines

Language: Python - Size: 10.7 KB - Last synced: 7 months ago - Pushed: almost 7 years ago - Stars: 0 - Forks: 1