Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Papers: 10.3390/metabo9100200
https://doi.org/10.3390/metabo9100200
The metaRbolomics Toolbox in Bioconductor and beyond
Cited by: 61
Author(s): Jan Stanstrup, Corey D. Broeckling, Rick Helmus, Nils Hoffmann, Ewy A. Mathé, Thomas Naake, Luca Nicolotti, Kristian Peters, Johannes Michael Rainer, Reza M. Salek, Tobias Schulze, Emma L. Schymanski, Michael A. Stravs, Etienne Thévenot, Hendrik Treutler, Ralf Weber, Egon Willighagen, Michael Witting, Steffen Neumann
Published: about 5 years ago
Software Mentions 92
bioconductor: alsace
Papers that mentioned: 1bioconductor: BiGGR
Constraint based modeling in R using metabolic reconstruction databasesPapers that mentioned: 4
bioconductor: BridgeDbR
Code for using BridgeDb identifier mapping framework from within RPapers that mentioned: 4
bioconductor: CAMERA
Collection of annotation related methods for mass spectrometry dataPapers that mentioned: 429
bioconductor: ChemmineOB
R interface to a subset of OpenBabel functionalitiesPapers that mentioned: 4
bioconductor: CluMSID
Clustering of MS2 Spectra for Metabolite IdentificationPapers that mentioned: 1
bioconductor: graphite
GRAPH Interaction from pathway Topological EnvironmentPapers that mentioned: 30
bioconductor: KEGGgraph
KEGGgraph: A graph approach to KEGG PATHWAY in R and BioconductorPapers that mentioned: 39
bioconductor: KEGGREST
Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)Papers that mentioned: 75
bioconductor: LOBSTAHS
Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy SequencesPapers that mentioned: 5
bioconductor: MassSpecWavelet
Peak Detection for Mass Spectrometry data using wavelet-based algorithmsPapers that mentioned: 19
bioconductor: MetCirc
Navigating mass spectral similarity in high-resolution MS/MS metabolomics data metabolomics dataPapers that mentioned: 3
bioconductor: MetNet
Inferring metabolic networks from untargeted high-resolution mass spectrometry dataPapers that mentioned: 15
bioconductor: MSnbase
Base Functions and Classes for Mass Spectrometry and ProteomicsPapers that mentioned: 24
bioconductor: msPurity
Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in MetabolomicsPapers that mentioned: 2
bioconductor: mzR
parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass spectrometry data)Papers that mentioned: 12
bioconductor: pathview
a tool set for pathway based data integration and visualizationPapers that mentioned: 144
bioconductor: pathwayPCA
Integrative Pathway Analysis with Modern PCA Methodology and Gene SelectionPapers that mentioned: 4
bioconductor: paxtoolsr
Access Pathways from Multiple Databases Through BioPAX and Pathway CommonsPapers that mentioned: 3
bioconductor: PSICQUIC
Papers that mentioned: 75bioconductor: RedeR
Interactive visualization and manipulation of nested networksPapers that mentioned: 21
bioconductor: RMassBank
Workflow to process tandem MS files and build MassBank recordsPapers that mentioned: 10
bioconductor: ropls
PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics dataPapers that mentioned: 81
bioconductor: rWikiPathways
rWikiPathways - R client library for the WikiPathways APIPapers that mentioned: 2
bioconductor: SDAMS
Differential Abundant/Expression Analysis for Metabolomics, Proteomics and single-cell RNA sequencing DataPapers that mentioned: 2
bioconductor: SPIA
Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbationsPapers that mentioned: 155
bioconductor: STATegRa
Classes and methods for multi-omics data integrationPapers that mentioned: 7
bioconductor: TargetSearch
A package for the analysis of GC-MS metabolite profiling dataPapers that mentioned: 34
cran: DiffCorr
Analyzing and Visualizing Differential Correlation Networks in Biological DataPapers that mentioned: 21
cran: enviPat
Isotope Pattern, Profile and Centroid Calculation for Mass SpectrometryPapers that mentioned: 10
cran: ggplot2
Create Elegant Data Visualisations Using the Grammar of GraphicsPapers that mentioned: 11,441
cran: hyperSpec
Work with Hyperspectral Data, i.e. Spectra + Meta Information (Spatial, Time, Concentration, ...)Papers that mentioned: 24
cran: nontarget
Papers that mentioned: 2cran: osd
Orthogonal Signal Deconvolution for Spectra Deconvolution in GC-MS and GCxGC-MS DataPapers that mentioned: 1
cran: RAMClustR
Mass Spectrometry Metabolomics Feature Clustering and InterpretationPapers that mentioned: 11
cran: speaq
Tools for Nuclear Magnetic Resonance (NMR) Spectra Alignment, Peak Based Processing, Quantitative Analysis and VisualizationsPapers that mentioned: 5
cran: specmine
Papers that mentioned: 4cran: tmod
Feature Set Enrichment Analysis for Metabolomics and TranscriptomicsPapers that mentioned: 18
pypi: graphite
Papers that mentioned: 30pypi: metaMS
Data processing, and annotation for metabolomics analysis by low-resolution GC-MSPapers that mentioned: 13
pypi: xcms
calculated extended contact mode score provided the query and template protein-ligand structuresPapers that mentioned: 68