PanomiR

DOI: 10.18129/B9.bioc.PanomiR  

Detection of miRNAs that regulate interacting groups of pathways

Bioconductor version: Release (3.16)

PanomiR is a package to detect miRNAs that target groups of pathways from gene expression data. This package provides functionality for generating pathway activity profiles, determining differentially activated pathways between user-specified conditions, determining clusters of pathways via the PCxN package, and generating miRNAs targeting clusters of pathways. These function can be used separately or sequentially to analyze RNA-Seq data.

Author: Pourya Naderi [aut, cre], Yue Yang (Alan) Teo [aut], Ilya Sytchev [aut], Winston Hide [aut]

Maintainer: Pourya Naderi <pouryany at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("PanomiR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("PanomiR")

 

HTML	R Script	PanomiR Tutorial
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	GeneExpression, GeneSetEnrichment, GeneTarget, Pathways, Software, miRNA
Version	1.2.0
In Bioconductor since	BioC 3.15 (R-4.2) (1 year)
License	MIT + file LICENSE
Depends	R (>= 4.2.0)
Imports	clusterProfiler, dplyr, forcats, GSEABase, igraph, limma, metap, org.Hs.eg.db, parallel, preprocessCore, RColorBrewer, rlang, tibble, withr, utils
LinkingTo
Suggests	testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/pouryany/PanomiR
BugReports	https://github.com/pouryany/PanomiR/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	PanomiR_1.2.0.tar.gz
Windows Binary	PanomiR_1.2.0.zip
macOS Binary (x86_64)	PanomiR_1.2.0.tgz
macOS Binary (arm64)	PanomiR_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/PanomiR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/PanomiR
Bioc Package Browser	https://code.bioconductor.org/browse/PanomiR/
Package Short Url	https://bioconductor.org/packages/PanomiR/
Package Downloads Report	Download Stats