PanomiR
This is the released version of PanomiR; for the devel version, see PanomiR.
Detection of miRNAs that regulate interacting groups of pathways
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.16.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (4.5 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_1.16.0.tar.gz |
| Windows Binary (x86_64) | PanomiR_1.16.0.zip |
| macOS Binary (big-sur-x86_64) | PanomiR_1.16.0.tgz |
| macOS Binary (sonoma-arm64) | PanomiR_1.16.0.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 |