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PanomiR

This is the development version of PanomiR; for the stable release version, see PanomiR.

Detection of miRNAs that regulate interacting groups of pathways

Bioconductor version: Development (3.18)

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>

Citation (from within R, enter citation("PanomiR")):

Installation

To install this package, start R (version "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews GeneExpression, GeneSetEnrichment, GeneTarget, Pathways, Software, miRNA
Version 1.5.0
In Bioconductor since BioC 3.15 (R-4.2) (1.5 years)
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
Linking To
Suggests testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown
System Requirements
Enhances
URL https://github.com/pouryany/PanomiR
Bug Reports https://github.com/pouryany/PanomiR/issues
See More
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Package Archives

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

Source Package PanomiR_1.5.0.tar.gz
Windows Binary PanomiR_1.5.0.zip
macOS Binary (x86_64) PanomiR_1.5.0.tgz
macOS Binary (arm64) PanomiR_1.5.0.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