Package: mirIntegrator 1.43.0

Diana Diaz

mirIntegrator: Integrating microRNA expression into signaling pathways for pathway analysis

Tools for augmenting signaling pathways to perform pathway analysis of microRNA and mRNA expression levels.

Authors:Diana Diaz <dmd at wayne dot edu>

mirIntegrator_1.43.0.tar.gz
mirIntegrator_1.43.0.zip(r-4.7)mirIntegrator_1.43.0.zip(r-4.6)mirIntegrator_1.43.0.zip(r-4.5)
mirIntegrator_1.43.0.tgz(r-4.6-any)mirIntegrator_1.43.0.tgz(r-4.5-any)
mirIntegrator_1.43.0.tar.gz(r-4.7-any)mirIntegrator_1.43.0.tar.gz(r-4.6-any)
mirIntegrator_1.43.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
mirIntegrator/json (API)

# Install 'mirIntegrator' in R:

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

Bug tracker:https://github.com/datad/mirintegrator/issues

Datasets:

augmented_pathways - Signaling pathways augmented with miRNA.
GSE43592_miRNA - Top table of preprocessed miRNA of GSE43592 dataset.
GSE43592_mRNA - Top table of preprocessed mRNA of GSE43592 dataset.
kegg_pathways - List of KEGG signaling pathways of human.
mirTarBase - MicroRNA-target interactions in human.
names_pathways - List of KEGG signaling pathways' names.

On BioConductor:mirIntegrator-1.43.0(bioc 3.24)mirIntegrator-1.42.0(bioc 3.23)

network microarray graphandnetwork pathways kegg

3.30 score 1 stars 2 scripts 5 exports 54 dependencies

Last updated from:f5e5e15868. Checks:1 FAILURE, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time	Files	Syslog
bioc-checks	FAILURE	231
linux-devel-x86_64	NOTE	309
source / vignettes	OK	237
linux-release-x86_64	NOTE	267
macos-release-arm64	NOTE	154
macos-oldrel-arm64	NOTE	195
windows-devel	NOTE	188
windows-release	NOTE	188
windows-oldrel	NOTE	185
wasm-release	OK	147

Exports:integrate_mir pathways2pdf plot_augmented_pathway plot_change smallest_pathway

Dependencies:AnnotationDbi askpass Biobase BiocGenerics Biostrings bit bit64 bitops blob boot cachem cli cpp11 crayon curl DBI farver fastmap generics ggplot2 glue graph gtable httr IRanges isoband jsonlite KEGGgraph KEGGREST labeling lifecycle memoise mime openssl org.Hs.eg.db pkgconfig png R6 RColorBrewer RCurl Rgraphviz rlang ROntoTools RSQLite S4Vectors S7 scales Seqinfo sys vctrs viridisLite withr XML XVector

mirIntegrator Overview

Integration of miRNA into signaling pathways | Graphical output | Pathway analysis of miRNA and mRNA: a case study | Citing mirIntegrator

Rendered frommirIntegrator.Rnwusingutils::Sweave

Last update: 2016-07-02
Started: 2015-06-09

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Signaling pathways augmented with miRNA.	augmented_pathways
Top table of preprocessed miRNA of GSE43592 dataset.	GSE43592_miRNA
Top table of preprocessed mRNA of GSE43592 dataset.	GSE43592_mRNA
Produce augmented pathways	integrate_mir
List of KEGG signaling pathways of human.	kegg_pathways
MicroRNA-target interactions in human.	mirTarBase
List of KEGG signaling pathways' names.	names_pathways
Export augmented pathways to pdf	pathways2pdf
Plotting of augmented pathway	plot_augmented_pathway
Plotting the change in pathways order	plot_change
Get the smallest pathway	smallest_pathway

Usage by other packages (reverse dependencies)