BioCor
This is the development version of BioCor; for the stable release version, see BioCor.
Functional Similarities
Bioconductor version: Development (3.24)
Calculates functional similarities based on the pathways described on KEGG and REACTOME or in gene sets. These similarities can be calculated for pathways or gene sets, genes, or clusters and combined with other similarities. They can be used to improve networks, gene selection, testing relationships...
Author: Lluís Revilla Sancho [aut, cre]
, Pau Sancho-Bru [ths]
, Juan José Salvatella Lozano [ths]
Maintainer: Lluís Revilla Sancho <lluis.revilla at gmail.com>
citation("BioCor")):
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("BioCor")
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("BioCor")| About BioCor | HTML | R Script |
| Advanced usage of BioCor | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Clustering, GeneExpression, Network, NetworkEnrichment, Pathways, Software, StatisticalMethod, SystemsBiology |
| Version | 1.37.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (9.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.4) |
| Imports | BiocParallel, GSEABase, Matrix, methods |
| System Requirements | |
| URL | https://bioconductor.org/packages/BioCor https://biocor.llrs.dev |
| Bug Reports | https://github.com/llrs/BioCor/issues |
See More
| Suggests | airway, BiocStyle, boot, DESeq2, ggplot2 (>= 3.4.1), GOSemSim, Hmisc, knitr (>= 1.43), org.Hs.eg.db, reactome.db, rmarkdown, spelling, testthat (>= 3.1.5), WGCNA |
| 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 | BioCor_1.37.0.tar.gz |
| Windows Binary (x86_64) | BioCor_1.37.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | BioCor_1.37.0.tgz |
| macOS Binary (sonoma-arm64) | BioCor_1.37.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/BioCor |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/BioCor |
| Bioc Package Browser | https://code.bioconductor.org/browse/BioCor/ |
| Package Short Url | https://bioconductor.org/packages/BioCor/ |
| Package Downloads Report | Download Stats |