eugenemel/maven_core

MAVEN: Core Libraries

Language: C++ - Size: 4.33 MB - Last synced: about 4 hours ago - Pushed: about 5 hours ago - Stars: 3 - Forks: 2

sajadamouei/classification-metabolomics

Implementation of a comparative analysis to find the best ML model for classifying dry eye disease from healthy controls using metabolomics datasets.

Language: Jupyter Notebook - Size: 10.5 MB - Last synced: about 6 hours ago - Pushed: about 7 hours ago - Stars: 0 - Forks: 0

eugenemel/maven

Maven GUI: Metabolomics Analysis and Visualization Engine

Language: C++ - Size: 5.42 MB - Last synced: about 8 hours ago - Pushed: about 12 hours ago - Stars: 18 - Forks: 9

PangeAI/cudams

GPU accelerated MatchMS

Language: Jupyter Notebook - Size: 4.97 MB - Last synced: about 6 hours ago - Pushed: about 15 hours ago - Stars: 0 - Forks: 0

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: 16 MB - Last synced: about 18 hours ago - Pushed: about 19 hours ago - Stars: 11 - Forks: 5

claudiavicente/MSPSCR

Metabolic state prediction at single-cell resolution is a project developed as a Bachelor's Thesis (TFG), to recover metabolic states from single-cell expression data.

Language: Jupyter Notebook - Size: 29.7 MB - Last synced: about 16 hours ago - Pushed: about 19 hours ago - Stars: 0 - Forks: 0

CNIC-Proteomics/TurboPutative-web

Language: HTML - Size: 257 MB - Last synced: about 9 hours ago - Pushed: about 19 hours ago - Stars: 0 - Forks: 0

lifs-tools/jgoslin

Java implementation of the latest shorthand nomenclature.

Language: Java - Size: 18.9 MB - Last synced: about 23 hours ago - Pushed: 1 day ago - Stars: 4 - Forks: 0

pyQms/pyqms

pyQms, generalized, fast and accurate mass spectrometry data quantification

Language: Python - Size: 1.93 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 28 - Forks: 9

metgem/metgem

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

Language: Python - Size: 18.5 MB - Last synced: 3 days ago - Pushed: 4 days ago - Stars: 28 - Forks: 3

p2m2/EP2M2

Metabolomics target analyzes manager

Language: Vue - Size: 8.11 MB - Last synced: 3 days ago - Pushed: 4 days ago - Stars: 1 - Forks: 1

yufree/pmd

Paired Mass Distance(PMD) analysis for GC/LC-MS based nontarget analysis

Language: R - Size: 78.7 MB - Last synced: about 12 hours ago - Pushed: 1 day ago - Stars: 9 - Forks: 0

rformassspectrometry/ProtGenerics

S4 generic functions for Bioconductor mass spectrometry infrastructure

Language: R - Size: 95.7 KB - Last synced: 22 days ago - Pushed: 3 months ago - Stars: 7 - Forks: 5

hancockinformatics/MetaBridgeShiny

Repository for the MetaBridge Shiny app.

Language: R - Size: 115 MB - Last synced: 16 days ago - Pushed: 16 days ago - Stars: 2 - Forks: 0

yufree/rmwf

Reproducilble Metabolomics Workflow

Language: R - Size: 527 MB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 7 - Forks: 2

JoeRothwell/Molecular-epi

Data analysis for colorectal cancer projects, mainly using metabolomics data.

Language: R - Size: 872 KB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 4 - Forks: 0

nara3m/nara3m

Nara Marella

Size: 33.2 KB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 0 - Forks: 0

hhabra/metabCombiner

metabCombiner R Package: Paired Untargeted Metabolomics Feature Matching & Data Concatenation

Language: R - Size: 2.91 MB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 9 - Forks: 2

rformassspectrometry/CompoundDb

Creating and using (chemical) compound databases

Language: R - Size: 13.9 MB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 16 - Forks: 14

microbiomedata/nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model

Language: Python - Size: 117 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 26 - Forks: 8

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: 3 days ago - Pushed: 3 days ago - Stars: 5 - Forks: 0

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: 3.58 MB - Last synced: 3 days ago - Pushed: 4 days ago - Stars: 3 - Forks: 1

EBI-Metabolights/SAFERnmr

Language: R - Size: 69.3 MB - Last synced: 3 days ago - Pushed: 4 days ago - Stars: 4 - 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: 15 - Forks: 2

glasgowcompbio/vimms

A programmable and modular LC/MS simulator in Python

Language: Python - Size: 288 MB - Last synced: 5 days ago - Pushed: about 1 month ago - Stars: 17 - Forks: 7

MoTrPAC/MotrpacBicQC

R package for the MoTrPAC community

Language: R - Size: 3.64 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 8 - Forks: 4

pnnl/isicle

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

Language: Python - Size: 19.7 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 57 - Forks: 19

computational-metabolomics/dimspy

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

Language: Python - Size: 107 MB - Last synced: 10 days ago - Pushed: 11 months ago - Stars: 18 - Forks: 9

rformassspectrometry/Spectra

Low level infrastructure to handle MS spectra

Language: R - Size: 19.3 MB - Last synced: 10 days ago - Pushed: 10 days ago - Stars: 31 - Forks: 23

AHuffmyer/SymbioticIntegration

Symbiotic nutritional exchange in coral larvae under thermal stress

Size: 180 MB - Last synced: 10 days ago - Pushed: 10 days ago - Stars: 0 - Forks: 0

EMSL-Computing/CoreMS

CoreMS is a comprehensive mass spectrometry software framework

Language: Python - Size: 278 MB - Last synced: 10 days ago - Pushed: 10 days ago - Stars: 47 - Forks: 25

AHuffmyer/EarlyLifeHistory_Energetics

Ontogenetic shifts in symbiotic and metabolic state in coral early life history

Language: HTML - Size: 466 MB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 5 - Forks: 1

cran-task-views/Omics

CRAN Task View: Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Size: 73.2 KB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 15 - Forks: 4

Meredith-Lab/volcalc

volcalc: Calculate Volatility of Chemical Compounds

Language: R - Size: 4.6 MB - Last synced: 11 days ago - Pushed: 22 days ago - Stars: 4 - Forks: 1

CCMS-UCSD/GNPSDocumentation

Documentation for GNPS and related tools as written in mkdocs

Language: HTML - Size: 248 MB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 34 - Forks: 80

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: 22 days ago - Pushed: 22 days ago - Stars: 75 - Forks: 17

jorainer/xcmsTutorials

Tutorials and workshops describing LC-MS(/MS) data pre-processing and analysis using the xcms Bioconductor package

Language: TeX - Size: 32.4 MB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 5 - Forks: 1

mapp-metabolomics-unit/met-annot-unifier

A Python package to handle metabolite annotation tables (GNPS, ISDB and Sirius)

Language: Python - Size: 4.15 MB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 0 - Forks: 0

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: 119 MB - Last synced: 15 days ago - Pushed: 15 days ago - Stars: 0 - Forks: 1

lifs-tools/.github

LIFS Tools Overview

Size: 37.1 KB - Last synced: 15 days ago - Pushed: 7 months ago - Stars: 0 - 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: 16 days ago - Pushed: 16 days ago - Stars: 3 - Forks: 2

lifs-tools/goslin

Goslin is the Grammar on succinct lipid nomenclature.

Language: ANTLR - Size: 7.2 MB - Last synced: 16 days ago - Pushed: 16 days ago - Stars: 10 - Forks: 1

rformassspectrometry/MetaboAnnotation

High level functionality to support and simplify metabolomics data annotation.

Language: R - Size: 12.4 MB - Last synced: 15 days ago - Pushed: 16 days ago - Stars: 11 - Forks: 9

czbiohub-sf/Rapid-QC-MS

Realtime quality control for mass spectrometry data acquisition

Language: Python - Size: 4.4 MB - Last synced: 13 days ago - Pushed: about 1 month ago - Stars: 12 - Forks: 2

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: 16 days ago - Pushed: 17 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: 18 days ago - Pushed: 18 days ago - Stars: 1 - 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: 16 days ago - Pushed: 18 days ago - Stars: 0 - Forks: 0

rformassspectrometry/QFeatures

Quantitative features for mass spectrometry data

Language: R - Size: 21.4 MB - Last synced: 18 days ago - Pushed: 18 days ago - Stars: 21 - Forks: 6

Metaboverse/Metaboverse

Visualization and analysis platform for metabolic data and network pattern recognition

Language: JavaScript - Size: 511 MB - Last synced: 18 days ago - Pushed: 18 days ago - Stars: 38 - Forks: 6

pcastellanoescuder/POMAcounts

:apple: Web-based Application for Exploratory and Statistical Analysis of Mass Spectrometry Spectral Counts Data

Language: R - Size: 303 KB - Last synced: 20 days ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 0

pcastellanoescuder/fobitoolsGUI

:mag_right: Web-based Tool for Interacting with FOBI Ontology

Language: R - Size: 625 KB - Last synced: 20 days ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 2

BiRG/pyopls

A Python 3 implementation of orthogonal projection to latent structures

Language: Python - Size: 1.69 MB - Last synced: 11 days ago - Pushed: 3 months ago - Stars: 56 - Forks: 16

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: 22 days ago - Pushed: 22 days ago - Stars: 15 - Forks: 3

wfondrie/depthcharge

A deep learning toolkit for mass spectrometry

Language: Python - Size: 1.29 MB - Last synced: 21 days ago - Pushed: 22 days ago - Stars: 51 - Forks: 16

yufree/xcmsrocker

Rocker image for metabolomics data analysis

Language: HTML - Size: 1000 KB - Last synced: about 1 month ago - Pushed: 3 months ago - Stars: 12 - Forks: 3

cbib/DIMet

Differential analysis of targeted Isotope-labeled Metabolomics data

Language: Python - Size: 475 KB - Last synced: 23 days ago - Pushed: 23 days ago - Stars: 3 - Forks: 2

plyush1993/OUKS

🔴OUKS🔵 Omics Untargeted Key Script

Language: R - Size: 30.4 MB - Last synced: 23 days ago - Pushed: 23 days ago - Stars: 8 - Forks: 2

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: 24 days ago - Pushed: 24 days ago - Stars: 13 - Forks: 6

matchms/matchms

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

Language: Python - Size: 38 MB - Last synced: 28 days ago - Pushed: 29 days ago - Stars: 165 - Forks: 57

xieguigang/mesh

MSdata expression matrix simulator for test metabolomics analysis pipeline

Language: HTML - Size: 65.5 MB - Last synced: 25 days ago - Pushed: 25 days ago - Stars: 6 - Forks: 2

thbuerg/MetabolomicsCommonDiseases

⛑ Code for "Metabolomic profiles predict individual multi-disease outcomes" ⛑

Language: Jupyter Notebook - Size: 1.5 MB - Last synced: 18 days ago - Pushed: over 1 year ago - Stars: 14 - Forks: 1

himelmallick/IntegratedLearner

Integrated Machine Learning for Multi-omics Classification and Prediction

Language: HTML - Size: 22.1 MB - Last synced: 22 days ago - Pushed: about 2 months ago - Stars: 11 - Forks: 4

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: 30 days ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

rformassspectrometry/MetaboCoreUtils

Core utilities for metabolomics.

Language: R - Size: 13.4 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 7 - Forks: 6

computational-metabolomics/structToolbox

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

Language: R - Size: 24.7 MB - Last synced: 29 days ago - Pushed: 4 months ago - Stars: 8 - Forks: 4

mapio/jp2rt

A Java and Python package to Predict Retention Times

Language: Java - Size: 286 KB - Last synced: 29 days ago - Pushed: about 2 months ago - Stars: 3 - Forks: 0

2n3m/2n3m

Biomedicine, Pharma, Life Science, IT Consulting

Size: 68.4 KB - Last synced: 11 days ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

glasgowcompbio/pyMultiOmics

Python toolbox for multi-omics data mapping and analysis

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

yufree/metaworkflow

Online workflow guidelines for metabolomics

Language: TeX - Size: 33.2 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 23 - Forks: 10

phenomecentre/peakPantheR

On-instrument and post-acquisition targeted feature extraction

Language: R - Size: 4.51 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 12 - Forks: 1

lucinamay/biosynfoni

a *biosynformatic* fingerprint to explore natural product distance and diversity

Language: Python - Size: 11.1 MB - Last synced: 16 days ago - Pushed: 17 days ago - Stars: 8 - Forks: 1

tornikeo/cudams

CUDA-accelerated MatchMS

Language: Jupyter Notebook - Size: 16.1 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 0 - Forks: 0

CooperstoneLab/MS2extract

R package to create in-house MS/MS compound libraries

Language: R - Size: 38.3 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 5 - Forks: 0

tnaake/MatrixQCvis

Language: R - Size: 4.47 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 5 - Forks: 1

Omicometrics/pypls

Implementation of PLS-DA and OPLS-DA for high dimensional data, like MS in metabolomics.

Language: Python - Size: 146 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 19 - Forks: 3

ethanbass/chromConverter

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

Language: R - Size: 6.74 MB - Last synced: about 1 month ago - Pushed: 2 months ago - Stars: 23 - Forks: 3

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 2 months ago - Pushed: about 2 months ago - Stars: 11 - Forks: 2

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: about 1 month ago - Pushed: about 1 month ago - Stars: 1 - Forks: 0

rformassspectrometry/MsCoreUtils

Core Utils for Mass Spectrometry Data

Language: R - Size: 12.5 MB - Last synced: 10 days ago - Pushed: about 1 month ago - Stars: 16 - Forks: 11

DTUComputeStatisticsAndDataAnalysis/MBPLS

(Multiblock) Partial Least Squares Regression for Python

Language: Python - Size: 16.6 MB - Last synced: 21 days ago - Pushed: over 4 years ago - Stars: 28 - Forks: 8

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: about 1 month ago - Pushed: about 2 months ago - Stars: 44 - Forks: 14

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 2 months ago - Pushed: about 2 months ago - Stars: 14 - Forks: 8

opencobra/cobratoolbox

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

Language: MATLAB - Size: 1.02 GB - Last synced: 30 days ago - Pushed: about 1 month ago - Stars: 237 - Forks: 303

EMSL-Computing/IonToolPack

A software tool for omics-agnostic automated quality control of mass spectrometry data.

Language: Python - Size: 460 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

metaspace2020/metaspace

Cloud engine and platform for metabolite annotation for imaging mass spectrometry

Language: TypeScript - Size: 71.1 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 42 - Forks: 8

OpenMS/OpenMS

The codebase of the OpenMS project

Language: C++ - Size: 609 MB - Last synced: about 2 months ago - Pushed: about 2 months 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 2 months ago - Pushed: about 2 months ago - Stars: 15 - Forks: 14

griquelme/tidyms

TidyMS: Tools for working with MS data in untargeted metabolomics

Language: Python - Size: 30.3 MB - Last synced: 2 months ago - Pushed: 3 months ago - Stars: 49 - Forks: 11

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 2 months ago - Pushed: about 2 months 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 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

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 2 months ago - Pushed: about 2 months ago - Stars: 2 - Forks: 0

AberystwythSystemsBiology/pyMEAN

A Python package for metabolite enrichment analysis.

Language: Python - Size: 114 KB - Last synced: 11 days ago - Pushed: about 2 years ago - Stars: 8 - Forks: 2

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: 10 days ago - Pushed: 10 days ago - Stars: 14 - Forks: 6

omicsEye/massSight

An R package for the alignment and scaling of LC-MS metabolomics data

Language: R - Size: 13.5 MB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 2 - Forks: 0

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 2 months ago - Pushed: about 2 months ago - Stars: 12 - Forks: 2

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: 2 months ago - Pushed: 2 months ago - Stars: 22 - Forks: 8

egonw/metabolomics-practical

Size: 327 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 1 - 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: about 1 month ago - Pushed: 2 months ago - Stars: 15 - Forks: 2

EuBIC/ReproducibleMSGuidelines

This project aims at defining a set of guidelines for reproducible mass spectrometry-based experiments.

Language: JavaScript - Size: 332 KB - Last synced: 3 months ago - Pushed: 8 months ago - Stars: 6 - Forks: 1

idslme/IDSL.IPA

Intrinsic Peak Analysis (IPA) pipeline for peak-picking in large-scale untargeted small molecule analysis including metabolomics, lipidomics, exposomics, and environmental studies.

Language: R - Size: 17.1 MB - Last synced: 11 days ago - Pushed: almost 1 year ago - Stars: 14 - Forks: 1