mirIntegrator: Integrating microRNA expression into signaling pathways for pathway analysis

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

Author
Diana Diaz <dmd at wayne dot edu>
Date of publication
None
Maintainer
Diana Diaz <dmd@wayne.edu>
License
GPL (>=3)
Version
1.4.0
URLs

View on Bioconductor

Man pages

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.
integrate_mir
Produce augmented pathways
kegg_pathways
List of KEGG signaling pathways of human.
mirTarBase
MicroRNA-target interactions in human.
names_pathways
List of KEGG signaling pathways' names.
pathways2pdf
Export augmented pathways to pdf
plot_augmented_pathway
Plotting of augmented pathway
plot_change
Plotting the change in pathways order
smallest_pathway
Get the smallest pathway

Files in this package

mirIntegrator/DESCRIPTION
mirIntegrator/NAMESPACE
mirIntegrator/R
mirIntegrator/R/augment_pathways.R
mirIntegrator/R/plot_pathways.R
mirIntegrator/R/view_pathways.R
mirIntegrator/build
mirIntegrator/build/vignette.rds
mirIntegrator/data
mirIntegrator/data/GSE43592_mRNA.rda
mirIntegrator/data/GSE43592_miRNA.rda
mirIntegrator/data/augmented_pathways.rda
mirIntegrator/data/datalist
mirIntegrator/data/kegg_pathways.rda
mirIntegrator/data/mirTarBase.rda
mirIntegrator/data/names_pathways.rda
mirIntegrator/inst
mirIntegrator/inst/NEWS
mirIntegrator/inst/doc
mirIntegrator/inst/doc/mirIntegrator.R
mirIntegrator/inst/doc/mirIntegrator.Rnw
mirIntegrator/inst/doc/mirIntegrator.pdf
mirIntegrator/inst/scripts
mirIntegrator/inst/scripts/get_augmented_pathways.R
mirIntegrator/inst/scripts/get_kegg_pathways.R
mirIntegrator/inst/scripts/get_mirTarBase.R
mirIntegrator/inst/scripts/get_names_pathways.R
mirIntegrator/inst/unitTests
mirIntegrator/inst/unitTests/test_datasets.R
mirIntegrator/inst/unitTests/test_integrate.R
mirIntegrator/man
mirIntegrator/man/GSE43592_mRNA.Rd
mirIntegrator/man/GSE43592_miRNA.Rd
mirIntegrator/man/augmented_pathways.Rd
mirIntegrator/man/integrate_mir.Rd
mirIntegrator/man/kegg_pathways.Rd
mirIntegrator/man/mirTarBase.Rd
mirIntegrator/man/names_pathways.Rd
mirIntegrator/man/pathways2pdf.Rd
mirIntegrator/man/plot_augmented_pathway.Rd
mirIntegrator/man/plot_change.Rd
mirIntegrator/man/smallest_pathway.Rd
mirIntegrator/tests
mirIntegrator/tests/runTests.R
mirIntegrator/vignettes
mirIntegrator/vignettes/mirIntegrator.Rnw
mirIntegrator/vignettes/mirIntegrator.bib