CNIC-Proteomics/TurboPutative-web

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opencobra/cobratoolbox

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

Language: MATLAB - Size: 1.02 GB - Last synced: about 5 hours ago - Pushed: about 5 hours ago - Stars: 237 - Forks: 302

rformassspectrometry/MetaboAnnotation

High level functionality to support and simplify metabolomics data annotation.

Language: R - Size: 9.93 MB - Last synced: about 9 hours ago - Pushed: about 10 hours ago - Stars: 11 - Forks: 9

Metaboverse/Metaboverse

Visualization and analysis platform for metabolic data and network pattern recognition

Language: JavaScript - Size: 510 MB - Last synced: about 18 hours ago - Pushed: about 18 hours ago - Stars: 38 - Forks: 6

mapp-metabolomics-unit/met-annot-unifier

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

Language: Python - Size: 4.1 MB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 0 - Forks: 0

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: 2 days ago - Pushed: 8 months ago - Stars: 15 - Forks: 4

eugenemel/maven_core

MAVEN: Core Libraries

Language: C++ - Size: 4.04 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 3 - Forks: 2

eugenemel/maven

Maven GUI: Metabolomics Analysis and Visualization Engine

Language: C++ - Size: 5.16 MB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 18 - Forks: 9

microbiomedata/nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model

Language: Python - Size: 113 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 26 - Forks: 8

hancockinformatics/MetaBridgeShiny

Repository for the MetaBridge Shiny app.

Language: R - Size: 115 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 2 - Forks: 0

2n3m/2n3m

Biomedicine, Pharma, Life Science, IT Consulting

Size: 68.4 KB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 0 - Forks: 0

nara3m/nara3m

Nara Marella

Size: 30.3 KB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 0 - Forks: 0

wfondrie/depthcharge

A deep learning toolkit for mass spectrometry

Language: Python - Size: 1.47 MB - Last synced: 3 days ago - Pushed: 4 days ago - Stars: 51 - Forks: 16

lifs-tools/pygoslin

Python implementation of parsers for the Grammars on succinct lipid nomenclature (Goslin).

Language: Python - Size: 9.73 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 3 - Forks: 2

glasgowcompbio/pyMultiOmics

Python toolbox for multi-omics data mapping and analysis

Language: Jupyter Notebook - Size: 45.9 MB - Last synced: 4 days 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: 4 days ago - Pushed: 4 days ago - Stars: 23 - Forks: 10

EBI-Metabolights/SAFERnmr

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

phenomecentre/peakPantheR

On-instrument and post-acquisition targeted feature extraction

Language: R - Size: 4.51 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 12 - Forks: 1

tornikeo/cudams

CUDA-accelerated MatchMS

Language: Jupyter Notebook - Size: 15.5 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 0 - Forks: 0

EMSL-Computing/CoreMS

CoreMS is a comprehensive mass spectrometry software framework

Language: Python - Size: 278 MB - Last synced: 6 days ago - Pushed: 7 days ago - Stars: 46 - Forks: 25

CooperstoneLab/MS2extract

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

Language: R - Size: 38.3 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 5 - Forks: 0

tnaake/MatrixQCvis

Language: R - Size: 4.47 MB - Last synced: 17 days ago - Pushed: 17 days 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: 6 days ago - Pushed: 7 days 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: 6 days ago - Pushed: about 1 month 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: 15 days ago - Pushed: 17 days 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: 7 days ago - Pushed: 7 days ago - Stars: 1 - Forks: 0

lifs-tools/goslin

Goslin is the Grammar on succinct lipid nomenclature.

Language: ANTLR - Size: 7.17 MB - Last synced: 6 days ago - Pushed: 7 days ago - Stars: 10 - Forks: 1

rformassspectrometry/MsCoreUtils

Core Utils for Mass Spectrometry Data

Language: R - Size: 12.5 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 16 - Forks: 11

lifs-tools/cppgoslin

C++ implementation of parsers for the Grammars on succinct lipid nomenclature (Goslin).

Language: C++ - Size: 9.17 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 0 - Forks: 0

yufree/rmwf

Reproducilble Metabolomics Workflow

Language: R - Size: 527 MB - Last synced: 11 days ago - Pushed: 12 days ago - Stars: 7 - Forks: 2

yufree/pmd

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

Language: R - Size: 78.1 MB - Last synced: 11 days ago - Pushed: 12 days ago - Stars: 9 - Forks: 0

MetaSys-LISBP/IsoCor

IsoCor: Isotope Correction for mass spectrometry labeling experiments

Language: Python - Size: 2.39 MB - Last synced: 11 days ago - Pushed: 6 months ago - Stars: 24 - Forks: 8

matchms/matchms

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

Language: Python - Size: 38 MB - Last synced: 15 days ago - Pushed: 16 days ago - Stars: 163 - Forks: 56

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: 13 days ago - Pushed: 15 days 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: 14 days ago - Pushed: 17 days ago - Stars: 14 - Forks: 8

EMSL-Computing/IonToolPack

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

Language: Python - Size: 460 MB - Last synced: 14 days ago - Pushed: 14 days 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: 17 days ago - Pushed: 17 days ago - Stars: 42 - Forks: 8

OpenMS/OpenMS

The codebase of the OpenMS project

Language: C++ - Size: 609 MB - Last synced: 16 days ago - Pushed: 17 days 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: 17 days ago - Pushed: 17 days 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: about 1 month ago - Pushed: 2 months ago - Stars: 49 - Forks: 11

mapio/jp2rt

A Java and Python package to Predict Retention Times

Language: Java - Size: 286 KB - Last synced: 10 days ago - Pushed: 25 days ago - Stars: 4 - Forks: 0

rformassspectrometry/MetaboCoreUtils

Core utilities for metabolomics.

Language: R - Size: 13.4 MB - Last synced: 15 days ago - Pushed: 16 days ago - Stars: 7 - Forks: 6

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: 17 days ago - Pushed: 18 days ago - Stars: 2 - Forks: 1

Karnovsky-Lab/DNEA

DNEA is an R package to construct data-driven biological networks from -omics data.

Language: R - Size: 18.9 MB - Last synced: 14 days ago - Pushed: 14 days ago - Stars: 0 - Forks: 0

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: 20 days ago - Pushed: 21 days ago - Stars: 0 - Forks: 0

rformassspectrometry/Spectra

Low level infrastructure to handle MS spectra

Language: R - Size: 16.6 MB - Last synced: about 6 hours ago - Pushed: about 1 month ago - Stars: 31 - Forks: 23

ethanbass/mzinspectr

Load and analyze MS-DIAL alignment files in R for analysis of mass spectrometry data.

Language: R - Size: 160 KB - Last synced: 24 days ago - Pushed: 25 days ago - Stars: 2 - Forks: 0

himelmallick/IntegratedLearner

Integrated Machine Learning for Multi-omics Classification and Prediction

Language: HTML - Size: 22.1 MB - Last synced: 24 days ago - Pushed: 24 days ago - Stars: 9 - Forks: 4

pnnl/isicle

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

Language: Python - Size: 19.7 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 57 - Forks: 19

cran-task-views/Omics

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

Size: 72.3 KB - Last synced: 25 days ago - Pushed: 25 days ago - Stars: 15 - Forks: 4

AberystwythSystemsBiology/pyMEAN

A Python package for metabolite enrichment analysis.

Language: Python - Size: 114 KB - Last synced: 12 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: 7 days ago - Pushed: 7 days ago - Stars: 14 - Forks: 6

MoTrPAC/MotrpacBicQC

R package for the MoTrPAC community

Language: R - Size: 3.6 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 8 - Forks: 4

metgem/metgem

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

Language: Python - Size: 16.8 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 28 - Forks: 3

omicsEye/massSight

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

Language: R - Size: 13.5 MB - Last synced: 4 days ago - Pushed: 4 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: 23 days ago - Pushed: 24 days ago - Stars: 12 - Forks: 2

Meredith-Lab/volcalc

volcalc: Calculate Volatility of Chemical Compounds

Language: R - Size: 4.5 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 3 - Forks: 1

CCMS-UCSD/GNPSDocumentation

Documentation for GNPS and related tools as written in mkdocs

Language: HTML - Size: 248 MB - Last synced: 10 days ago - Pushed: 11 days ago - Stars: 34 - Forks: 80

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 1 month ago - Pushed: about 1 month ago - Stars: 22 - Forks: 8

egonw/metabolomics-practical

Size: 327 KB - Last synced: about 1 month ago - Pushed: about 1 month 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: 9 days ago - Pushed: about 1 month ago - Stars: 15 - Forks: 2

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: 117 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

EuBIC/ReproducibleMSGuidelines

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

Language: JavaScript - Size: 332 KB - Last synced: about 1 month ago - Pushed: 7 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: 9 days ago - Pushed: 11 months ago - Stars: 14 - Forks: 1

biobakery/melonnpan

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

Language: R - Size: 3.81 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 33 - Forks: 8

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: 34.7 MB - Last synced: 18 days ago - Pushed: 18 days ago - Stars: 10 - Forks: 1

p2m2/EP2M2

Metabolomics target analyzes manager

Language: Vue - Size: 8.04 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 1 - Forks: 1

lucinamay/biosynfoni

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

Language: Python - Size: 11 MB - Last synced: 25 days ago - Pushed: 25 days ago - Stars: 8 - Forks: 1

cbib/DIMet

Differential analysis of targeted Isotope-labeled Metabolomics data

Language: Python - Size: 475 KB - Last synced: 1 day ago - Pushed: about 1 month ago - Stars: 3 - Forks: 2

jorainer/xcmsTutorials

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

Language: TeX - Size: 31 MB - Last synced: 9 days ago - Pushed: 10 days ago - Stars: 5 - Forks: 1

YuxingLu613/HMKG-Human-Metabolome-Knowledge-Graph

The Knowledge Graph (KG) built using data from HMDB

Size: 6.64 MB - Last synced: 12 days ago - Pushed: 4 months ago - Stars: 5 - Forks: 0

czbiohub-sf/Rapid-QC-MS

Realtime quality control for mass spectrometry data acquisition

Language: Python - Size: 4.4 MB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 10 - Forks: 2

idslme/IDSL.MXP

A light weight and fast parser for reading mzML, mzXML and netCDF data files

Language: R - Size: 199 KB - Last synced: about 1 hour ago - Pushed: about 1 year ago - Stars: 5 - Forks: 0

tomszar/metabo_adni

Metabolomics data processing for the ADNI data sets

Language: Python - Size: 66.4 KB - Last synced: 20 days ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

EBI-Metagenomics/holofood-database

HoloFood is a project investigating sustainable food production through hologenomics. This Django app is the data portal where samples and other datasets from the project are made publicly available.

Language: Python - Size: 20.3 MB - Last synced: 14 days ago - Pushed: about 2 months ago - Stars: 1 - Forks: 0

CyprienGille/Supervised-Autoencoder

A supervised autoencoder with structured sparsity for efficient and informed clinical prognosis.

Language: Python - Size: 18.9 MB - Last synced: 5 days ago - Pushed: 10 months ago - Stars: 4 - Forks: 0

yufree/pmdda

reproducible repo for PMDDA paper

Language: HTML - Size: 1.25 GB - Last synced: 11 days ago - Pushed: over 2 years ago - Stars: 5 - Forks: 1

cwieder/py-ssPA

Single sample pathway analysis tools for omics data

Language: Jupyter Notebook - Size: 8.05 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 9 - Forks: 4

Harel-lab/APRT-sex-differences

Language: Jupyter Notebook - Size: 27.4 MB - Last synced: 18 days ago - Pushed: 11 months ago - Stars: 2 - Forks: 0

idslme/IDSL.UFA

United Formula Annotation (UFA) for LC-HRMS data

Language: R - Size: 3.17 MB - Last synced: 9 days ago - Pushed: 12 months ago - Stars: 7 - Forks: 1

tnaake/MsQuality

Language: R - Size: 19.2 MB - Last synced: 7 days ago - Pushed: 2 months ago - Stars: 7 - Forks: 0

yufree/enet

network analysis for exposure study

Language: R - Size: 3.53 MB - Last synced: 11 days ago - Pushed: about 2 years ago - Stars: 2 - Forks: 0

rformassspectrometry/book

R for Mass Spectrometry documentation

Language: TeX - Size: 16.3 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 8 - Forks: 5

MetaSys-LISBP/IsoSolve Fork of sgsokol/IsoSolve

Integration of isotopic measurements

Language: Python - Size: 1 MB - Last synced: 12 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: 12 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: 9 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: 12 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: 6 days ago - Pushed: 7 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: 14 days 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: 12 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: 2 days ago - Pushed: 7 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: 15 days ago - Pushed: almost 4 years ago - Stars: 3 - Forks: 1

bihealth/metaquac 📦

Metabolomics Targeted Quality Control

Language: R - Size: 1.96 MB - Last synced: 14 days ago - Pushed: over 2 years ago - Stars: 8 - Forks: 1

BiRG/pyopls

A Python 3 implementation of orthogonal projection to latent structures

Language: Python - Size: 1.69 MB - Last synced: 9 days ago - Pushed: 2 months ago - Stars: 55 - Forks: 16

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: 4.16 MB - Last synced: 11 days ago - Pushed: 12 days ago - Stars: 3 - Forks: 1

rformassspectrometry/QFeatures

Quantitative features for mass spectrometry data

Language: R - Size: 20.9 MB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 20 - Forks: 6

computational-metabolomics/structToolbox

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

Language: R - Size: 24.7 MB - Last synced: 27 days ago - Pushed: 3 months ago - Stars: 7 - Forks: 4

kmcluskey/FlyMet

A multi-omics web app for Drosophila tissues

Language: Python - Size: 25.9 MB - Last synced: 14 days 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: about 1 month ago - Pushed: over 1 year ago - Stars: 22 - Forks: 9

yufree/mdaw

Metabolomics Data Analysis Workshop slides

Language: JavaScript - Size: 898 KB - Last synced: 11 days ago - Pushed: over 4 years ago - Stars: 5 - Forks: 0