PanomiR
Detection of miRNAs that regulate interacting groups of pathways
Bioconductor version: Release (3.20)
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("PanomiR")):
Installation
To install this package, start R (version "4.4") 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")| PanomiR Tutorial | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneExpression, GeneSetEnrichment, GeneTarget, Pathways, Software, miRNA |
| Version | 1.10.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (2.5 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 |
| System Requirements | |
| URL | https://github.com/pouryany/PanomiR |
| Bug Reports | https://github.com/pouryany/PanomiR/issues |
See More
| Suggests | testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | PanomiR_1.10.0.tar.gz |
| Windows Binary (x86_64) | PanomiR_1.10.0.zip |
| macOS Binary (x86_64) | PanomiR_1.10.0.tgz |
| macOS Binary (arm64) | PanomiR_1.9.0.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 |