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Search results for metabolomics
metabolomics
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111 search results found
Openms
⭐
438
The codebase of the OpenMS project
Cobratoolbox
⭐
232
The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
Xcms
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160
This is the git repository matching the Bioconductor package xcms: LC/MS and GC/MS Data Analysis
Matchms
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153
Python library for processing (tandem) mass spectrometry data and for computing spectral similarities.
Elmaven
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80
LC-MS data processing tool for large-scale metabolomics experiments.
Sirius
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66
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)
Isicle
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49
In silico chemical library engine for high-accuracy chemical property prediction
Depthcharge
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47
A deep learning toolkit for mass spectrometry
Sirius Libs
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45
sirius-libs - Metabolomics mass spectrometry framework for molecular formula identification of small molecules written in Java
Mzkit
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42
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.
Corems
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42
CoreMS is a comprehensive mass spectrometry software framework
Gnps_workflows
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41
Public Workflows at GNPS
Metaspace
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39
Cloud engine and platform for metabolite annotation for imaging mass spectrometry
Tidyms
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36
TidyMS: Tools for working with MS data in untargeted metabolomics
Datest
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34
Compare different differential abundance and expression methods
Gnpsdocumentation
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32
Documentation for GNPS and related tools as written in mkdocs
Metaboverse
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31
Visualization and analysis platform for metabolic data and network pattern recognition
Spectra
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29
Low level infrastructure to handle MS spectra
Metgem
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26
Calculation and visualization of molecular networks based on t-SNE algorithm
Pyqms
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26
pyQms, generalized, fast and accurate mass spectrometry data quantification
Ili
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25
Web-based software for visualization of molecular maps in 2D and 3D
Q2 Qemistree
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24
Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".
Melonnpan
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24
Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles
Ms Cleanr
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24
Nmdc Schema
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23
This repository contains the LinkML specification for the NMDC schema and the artifacts generated by LinkML.
Rhermes
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22
RHermes is a semi-targeted metabolomics package to deeply characterize biological and environmental samples.
Isocor
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21
IsoCor: Isotope Correction for mass spectrometry labeling experiments
Tools Metabolomics
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21
Galaxy tools for metabolomics maintained by Workflow4Metabolomics
Chemrich
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19
Chemical Similarity Enrichment analysis of metabolomics datasets
Qfeatures
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19
Quantitative features for mass spectrometry data
Ark
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19
Go REST API to replace Genbank, Uniprot, Rhea, and CHEMBL
Npyc Toolbox
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18
The nPYc-Toolbox defines objects for representing, and implements functions to manipulate and display, metabolic profiling datasets.
Metaboseek
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18
Interactive software to analyze and browse mass spectrometry data
Chromconverter
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18
Parsers for chromatography data in R (HPLC-DAD/UV, GC-FID, MS)
Ms Mint
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17
Targeted metabolomics with Python
Fermo
⭐
17
Dashboard for analysis of liquid chromatography (tandem) mass spectrometry data.
Mscoreutils
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16
Core Utils for Mass Spectrometry Data
Maven
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16
Maven GUI: Metabolomics Analysis and Visualization Engine
Optimus
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15
Workflow for LC-MS feature analysis and spatial mapping
Omicssuite.github.io
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15
OmicsSuite website for releasing new version.
Compounddb
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15
Creating and using (chemical) compound databases
Pypls
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15
Implementation of PLS-DA and OPLS-DA for high dimensional data, like MS in metabolomics.
Metarbolomics Book
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15
The MetaRbolomics book. A review of R packages in BioC, CRAN, gitlab and github.
Mspurity
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15
R-package - Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics
Omics
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14
CRAN Task View: Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics
Commonmz
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14
A collection of common mz values found in mass spectrometry.
Metax
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14
metaX: a flexible and comprehensive software for processing omics data.
Envigcms
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14
GC/LC-MS data analysis for environmental science
Vimms
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13
A programmable and modular LC/MS simulator in Python
Peakpanther
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12
On-instrument and post-acquisition targeted feature extraction
Forum Diseaseschem
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12
A Knowledge Graph from public databases and scientific literature to extract associations between chemicals and diseases.
Foodbiomarkerontology
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12
🚀 Food-Biomarker Ontology defines the relationships between foods and their associated metabolites (biomarkers) through a formal ontology
Buddy_metabolomics
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12
Molecular formula discovery via bottom-up MS/MS interrogation
Pomashiny
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11
🍎 Web-based User-friendly Workflow for Metabolomics and Proteomics Data Analysis
Xcmsrocker
⭐
11
Rocker image for metabolomics data analysis
Msbuddy
⭐
11
a python package for molecular formula analysis in MS-based small molecule studies
Metaboigniter
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11
Pre-processing of mass spectrometry-based metabolomics data with quantification and identification based on MS1 and MS2 data.
Chromatographr
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11
Toolset for the reproducible analysis of chromatography data in R (HPLC-DAD/UV, GC-FID).
Secimtools
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10
A set of metabolomics tools for use in Galaxy
Mbpls
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10
(Multiblock) Partial Least Squares Regression for Python
Ms2ldaviz
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10
Substructural discovery in untargeted metabolomics data using LDA topic modelling.
Protein Contaminant Libraries For Dda And Dia Proteomics
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9
This project is created by the Hao Lab at the Chemistry Department in George Washington University, Washington, D.C..(Publication pending) This project aims to provide contaminant protein FASTA and spectral libraries that can be universally applied to DDA and DIA proteomics and freely accessible for the proteomics community.
Metaboannotation
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9
High level functionality to support and simplify metabolomics data annotation.
Beamspy
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9
BEAMSpy - Birmingham mEtabolite Annotation for Mass Spectrometry (Python Package)
Pymultiomics
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9
Python toolbox for multi-omics data mapping and analysis
Goslin
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9
Goslin is the Grammar on succinct lipid nomenclature.
Ontology For Nutritional Studies
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8
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.
Madbyte
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8
Metabolomics And Dereplication By Two-dimensional Experiments - MADByTE NMR Metabolomics Platform
Npdtools
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8
Natural Product Discovery tools -- a toolkit containing various pipelines for in silico analysis of natural product mass spectrometry data
Workflow4metabolomics
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8
Workflow4Metabolomics meta repository
Tarmet
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8
An R package and Shiny App for MS-Based Targeted Metabolic Analyses
Pmd
⭐
7
Paired Mass Distance(PMD) analysis for GC/LC-MS based nontarget analysis
Pymass
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7
Package for analyzing MS with Python
Py Sspa
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7
Single sample pathway analysis tools for omics data
Cyclobranch
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7
A tool for mass spectrometry data analysis.
Ouks
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7
🔴OUKS🔵 Omics Untargeted Key Script
George
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7
geoRge: a computational tool for stable isotope labelling detection in LC/MS-based untargeted metabolomics
Qc4metabolomics
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7
QC systems for metabolomics studies
Mwtab
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7
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.
Fiora
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7
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.
Classyfirer
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7
R Interface to the ClassyFire REST API
Metamapp
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7
R codes for creating metamapp graphs and files
Book
⭐
7
R for Mass Spectrometry documentation
Metabocoreutils
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7
Core utilities for metabolomics.
Pyopls
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6
A Python 3 implementation of orthogonal projection to latent structures
Metabridge_shiny
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6
🕸 Network-based multi-omic integration of metabolomics data.
Dimspy
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6
Python package for processing direct-infusion mass spectrometry-based metabolomics and lipidomics data
Metabolighter
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6
R Interface to the Metabolights REST API
Dimepy
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6
Python package for the high-throughput nontargeted metabolite fingerprinting of nominal mass direct injection mass spectrometry directly from mzML files.
Biodendro
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6
A package to cluster and visualise MS/MS spectral data
Metabolome Lipidome Msdial
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6
Guide to processing raw LCMS metabolomic and lipidomic data using MS-DIAL, followed by data pre-processing and secondary annotation (of metabolites) in R.
Integratedlearner
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6
Integrated Machine Learning for Multi-omics Classification and Prediction
Sm Engine
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6
Engine for metabolite annotation for imaging mass spectrometry
Metabcombiner
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6
metabCombiner R Package: Paired Untargeted Metabolomics Feature Matching & Data Concatenation
Reproduciblemsguidelines
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6
This project aims at defining a set of guidelines for reproducible mass spectrometry-based experiments.
Motrpacbicqc
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6
R package for the MoTrPAC community
Msquality
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6
Metaboannotationtutorials
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6
Examples and tutorials for the MetaboAnnotation, MetaboCoreUtils and CompoundDb R packages
Rmwf
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6
Reproducilble Metabolomics Workflow
Peakabro
⭐
5
Peaklist Annotator and Browser
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