PCAN
This is the released version of PCAN; for the devel version, see PCAN.
Phenotype Consensus ANalysis (PCAN)
Bioconductor version: Release (3.23)
Phenotypes comparison based on a pathway consensus approach. Assess the relationship between candidate genes and a set of phenotypes based on additional genes related to the candidate (e.g. Pathways or network neighbors).
Author: Matthew Page and Patrice Godard
Maintainer: Matthew Page <matthew.page at ucb.com> and Patrice Godard <patrice.godard at gmail.com>
citation("PCAN")):
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("PCAN")
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("PCAN")| Assessing gene relevance for a set of phenotypes | HTML | R Script |
| Reference Manual |
Details
| biocViews | Annotation, FunctionalPrediction, Genetics, Network, Pathways, Sequencing, Software, VariantAnnotation |
| Version | 1.40.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (10.5 years) |
| License | CC BY-NC-ND 4.0 |
| Depends | R (>= 3.3), BiocParallel |
| Imports | grDevices, stats |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, knitr, rmarkdown, reactome.db, STRINGdb |
| 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 | PCAN_1.40.0.tar.gz |
| Windows Binary (x86_64) | PCAN_1.40.0.zip |
| macOS Binary (big-sur-x86_64) | PCAN_1.40.0.tgz |
| macOS Binary (sonoma-arm64) | PCAN_1.40.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/PCAN |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/PCAN |
| Bioc Package Browser | https://code.bioconductor.org/browse/PCAN/ |
| Package Short Url | https://bioconductor.org/packages/PCAN/ |
| Package Downloads Report | Download Stats |