PANR
This is the development version of PANR; for the stable release version, see PANR.
Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations
Bioconductor version: Development (3.24)
This package provides S4 classes and methods for inferring functional gene networks with edges encoding posterior beliefs of gene association types and nodes encoding perturbation effects.
Author: Xin Wang <xin_wang at hms.harvard.edu>
Maintainer: Xin Wang <xin_wang at hms.harvard.edu>
citation("PANR")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("PANR")
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("PANR")| Main vignette:Posterior association network and enriched functional gene modules inferred from rich phenotypes of gene perturbations | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CellBasedAssays, Clustering, GraphAndNetwork, ImmunoOncology, NetworkInference, Software, Visualization |
| Version | 1.59.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) (15 years) |
| License | Artistic-2.0 |
| Depends | R (>= 2.14), igraph |
| Imports | graphics, grDevices, MASS, methods, pvclust, stats, utils, RedeR |
| System Requirements | |
| URL |
See More
| Suggests | snow |
| 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 | PANR_1.59.0.tar.gz |
| Windows Binary (x86_64) | PANR_1.59.0.zip |
| macOS Binary (big-sur-x86_64) | PANR_1.59.0.tgz |
| macOS Binary (sonoma-arm64) | PANR_1.59.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/PANR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/PANR |
| Bioc Package Browser | https://code.bioconductor.org/browse/PANR/ |
| Package Short Url | https://bioconductor.org/packages/PANR/ |
| Package Downloads Report | Download Stats |