miRNApath: miRNApath: Pathway Enrichment for miRNA Expression Data

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This package provides pathway enrichment techniques for miRNA expression data. Specifically, the set of methods handles the many-to-many relationship between miRNAs and the multiple genes they are predicted to target (and thus affect.) It also handles the gene-to-pathway relationships separately. Both steps are designed to preserve the additive effects of miRNAs on genes, many miRNAs affecting one gene, one miRNA affecting multiple genes, or many miRNAs affecting many genes.

Author
James M. Ward <jmw86069@gmail.com> with contributions from Yunling Shi, Cindy Richards, John P. Cogswell
Date of publication
None
Maintainer
James M. Ward <jmw86069@gmail.com>
License
LGPL-2.1
Version
1.34.0

View on Bioconductor

Man pages

checkColumns
Check data.frame for Required Columns
convertFoldChange
Converts Fold Change to Consistent Format
filtermirnapath
Filter miRNApath data
loadmirnapath
Load miRNApath Data
loadmirnapathways
Load gene to pathway associations for miRNApath
loadmirnatogene
Load miRNA to gene associations for miRNApath
mirnaobj
mirnaobj, an S4 object of class "mirnapath"
mirnapath-class
S4 class mirnapath and its "show" method
miRNApath-package
miRNApath: Pathway Enrichment for miRNA Expression Data
mirnaTable
Create miRNA Enrichment Summary Table as data.frame
runEnrichment
Perform gene set enrichment analysis on a miRNApath object

Files in this package

miRNApath/DESCRIPTION
miRNApath/NAMESPACE
miRNApath/NEWS
miRNApath/R
miRNApath/R/checkColumns.R
miRNApath/R/convertFoldChange.R
miRNApath/R/filtermirnapath.R
miRNApath/R/loadmirnapath.R
miRNApath/R/loadmirnapathways.R
miRNApath/R/loadmirnatogene.R
miRNApath/R/mirnaTable.R
miRNApath/R/runEnrichment.R
miRNApath/R/show.mirnapath.R
miRNApath/build
miRNApath/build/vignette.rds
miRNApath/data
miRNApath/data/mirnaobj.rda
miRNApath/inst
miRNApath/inst/CITATION
miRNApath/inst/doc
miRNApath/inst/doc/miRNApath.R
miRNApath/inst/doc/miRNApath.Rnw
miRNApath/inst/doc/miRNApath.pdf
miRNApath/inst/samples
miRNApath/inst/samples/ADmiRNA.pdf
miRNApath/man
miRNApath/man/checkColumns.Rd
miRNApath/man/convertFoldChange.Rd
miRNApath/man/filtermirnapath.Rd
miRNApath/man/loadmirnapath.Rd
miRNApath/man/loadmirnapathways.Rd
miRNApath/man/loadmirnatogene.Rd
miRNApath/man/miRNApath-package.Rd
miRNApath/man/mirnaTable.Rd
miRNApath/man/mirnaobj.Rd
miRNApath/man/mirnapath-class.Rd
miRNApath/man/runEnrichment.Rd
miRNApath/vignettes
miRNApath/vignettes/miRNApath.Rnw