Package: mirIntegrator 1.37.0

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_1.37.0.tar.gz
mirIntegrator_1.37.0.zip(r-4.5)mirIntegrator_1.37.0.zip(r-4.4)mirIntegrator_1.37.0.zip(r-4.3)
mirIntegrator_1.37.0.tgz(r-4.4-any)mirIntegrator_1.37.0.tgz(r-4.3-any)
mirIntegrator_1.37.0.tar.gz(r-4.5-noble)mirIntegrator_1.37.0.tar.gz(r-4.4-noble)
mirIntegrator_1.37.0.tgz(r-4.4-emscripten)mirIntegrator_1.37.0.tgz(r-4.3-emscripten)
mirIntegrator.pdf |mirIntegrator.html✨
mirIntegrator/json (API)
NEWS

# 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:

GSE43592_mRNA - Top table of preprocessed mRNA of GSE43592 dataset.
GSE43592_miRNA - Top table of preprocessed miRNA of GSE43592 dataset.
augmented_pathways - Signaling pathways augmented with miRNA.
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-1.35.0(bioc 3.20)mirIntegrator-1.34.0(bioc 3.19)

network microarray graphandnetwork pathways kegg

3.30 score 1 stars 2 scripts 206 downloads 5 exports 68 dependencies

Last updated 24 days agofrom:f0be6940d3. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	NOTE	Oct 31 2024
R-4.5-linux	NOTE	Oct 30 2024
R-4.4-win	NOTE	Oct 31 2024
R-4.4-mac	NOTE	Oct 31 2024
R-4.3-win	NOTE	Oct 31 2024
R-4.3-mac	NOTE	Oct 31 2024

Exports:integrate_mir pathways2pdf plot_augmented_pathway plot_change smallest_pathway

Dependencies:AnnotationDbi askpass Biobase BiocGenerics Biostrings bit bit64 bitops blob boot cachem cli colorspace cpp11 crayon curl DBI fansi farver fastmap GenomeInfoDb GenomeInfoDbData ggplot2 glue graph gtable httr IRanges isoband jsonlite KEGGgraph KEGGREST labeling lattice lifecycle magrittr MASS Matrix memoise mgcv mime munsell nlme openssl org.Hs.eg.db pillar pkgconfig plogr png R6 RColorBrewer RCurl Rgraphviz rlang ROntoTools RSQLite S4Vectors scales sys tibble UCSC.utils utf8 vctrs viridisLite withr XML XVector zlibbioc

mirIntegrator Overview

Rendered frommirIntegrator.Rnwusingutils::Sweaveon Oct 30 2024.

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)