Package: MetaboSignal 1.35.0

Andrea Rodriguez-Martinez

MetaboSignal: MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways

MetaboSignal is an R package that allows merging, analyzing and customizing metabolic and signaling KEGG pathways. It is a network-based approach designed to explore the topological relationship between genes (signaling- or enzymatic-genes) and metabolites, representing a powerful tool to investigate the genetic landscape and regulatory networks of metabolic phenotypes.

Authors:Andrea Rodriguez-Martinez, Rafael Ayala, Joram M. Posma, Ana L. Neves, Maryam Anwar, Jeremy K. Nicholson, Marc-Emmanuel Dumas

MetaboSignal_1.35.0.tar.gz
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MetaboSignal_1.35.0.tgz(r-4.4-any)MetaboSignal_1.35.0.tgz(r-4.3-any)
MetaboSignal_1.35.0.tar.gz(r-4.5-noble)MetaboSignal_1.35.0.tar.gz(r-4.4-noble)
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MetaboSignal.pdf |MetaboSignal.html✨
MetaboSignal/json (API)
NEWS

# Install 'MetaboSignal' in R:

install.packages('MetaboSignal', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

MetaboSignal_table - Example of MetaboSignal network-table
directionality_reactions - List of KEGG reactions with incorrect/inconsistent directionality
hpaNormalTissue - Expression profiles for proteins in human tissues
keggNet_example - KEGG network example
kegg_pathways - Examples of metabolic and signaling human KEGG pathways
mergedNet_example - Network containing KEGG, OmniPath and TRRUST interactions
ppiNet_example - Signaling-transduction network
regulatory_interactions - Regulatory interactions from OmniPath and TRRUST

On BioConductor:MetaboSignal-1.35.0(bioc 3.20)MetaboSignal-1.34.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

19 exports 1.08 score 188 dependencies 4 mentions

Last updated 2 months agofrom:4f711a3af7

Exports:MS_changeNames MS_convertGene MS_distances MS_exportCytoscape MS_findMappedNodes MS_getPathIds MS_keggFinder MS_keggNetwork MS_nodeBW MS_reactionNetwork MS_removeDrugs MS_removeNode MS_replaceNode MS_shortestPaths MS_shortestPathsNetwork MS_tissueFilter MS_topologyFilter MS2_mergeNetworks MS2_ppiNetwork

Dependencies:abind AnnotationDbi AnnotationFilter AnnotationHub askpass backports base64enc BH Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel BiocVersion biomaRt Biostrings bit bit64 bitops blob boot broom bslib cachem car carData checkmate chron circlize cli clue cluster codetools colorspace ComplexHeatmap cowplot cpp11 crayon curl data.table DBI dbplyr DelayedArray Deriv digest doBy doParallel dplyr EnsDb.Hsapiens.v75 ensembldb evaluate ExperimentHub fansi farver fastmap filelock fontawesome foreach foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges GetoptLong ggplot2 glm2 GlobalOptions glue graph gridExtra gsubfn gtable highr Hmisc hms hpar htmlTable htmltools htmlwidgets httr httr2 igraph IRanges isoband iterators jquerylib jsonlite KEGGgraph KEGGREST knitr labeling lambda.r lattice lazyeval lifecycle lme4 magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv microbenchmark mime minqa modelr munsell MWASTools mygene nlme nloptr nnet numDeriv openssl org.Hs.eg.db pbkrtest pillar pkgconfig plogr plyr png ppcor prettyunits progress ProtGenerics proto purrr quantreg qvalue R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl reshape2 restfulr Rgraphviz Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors sass scales shape snow SparseArray SparseM sqldf stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect tinytex txdbmaker UCSC.utils utf8 vctrs viridis viridisLite withr xfun XML xml2 XVector yaml zlibbioc

MetaboSignal

Rendered fromMetaboSignal.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2017-09-19
Started: 2016-09-12

MetaboSignal 2: merging KEGG with additional interaction resources

Rendered fromMetaboSignal2.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2017-09-19
Started: 2017-09-13

Help page	Topics
List of KEGG reactions with incorrect/inconsistent directionality	directionality_reactions
Expression profiles for proteins in human tissues	hpaNormalTissue
Examples of metabolic and signaling human KEGG pathways	kegg_pathways
KEGG network example	keggNet_example
Network containing KEGG, OmniPath and TRRUST interactions	mergedNet_example
Example of MetaboSignal network-table	MetaboSignal_table
Transform KEGG IDs into common names	MS_changeNames
Transform Entrez IDs or gene symbols into KEGG IDs	MS_convertGene
Calculate gene-metabolite distance matrix	MS_distances
Export network in cytoscape format	MS_exportCytoscape
Map gene IDs or metabolite IDs onto the network	MS_findMappedNodes
Get pathway identifiers of a given organism	MS_getPathIds
Get KEGG IDs for compounds, organisms or pathways	MS_keggFinder
Build MetaboSignal network-table	MS_keggNetwork
Get distribution of node betweeness	MS_nodeBW
Build reaction-compound network	MS_reactionNetwork
Remove edges containing drug nodes	MS_removeDrugs
Remove undesired nodes from the network	MS_removeNode
Replace nodes of the network	MS_replaceNode
Calculate shortest paths	MS_shortestPaths
Build shortest-path subnetwork	MS_shortestPathsNetwork
Filter network based on tissue expression data	MS_tissueFilter
Filter network based on distances or betweenness	MS_topologyFilter
Merge networks	MS2_mergeNetworks
Build signaling-transduction network	MS2_ppiNetwork
Signaling-transduction network	ppiNet_example
Regulatory interactions from OmniPath and TRRUST	regulatory_interactions

Package: MetaboSignal 1.35.0

MetaboSignal: MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways

MetaboSignal

MetaboSignal 2: merging KEGG with additional interaction resources

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)