iBBiG
This is the development version of iBBiG; for the stable release version, see iBBiG.
Iterative Binary Biclustering of Genesets
Bioconductor version: Development (3.24)
iBBiG is a bi-clustering algorithm which is optimizes for binary data analysis. We apply it to meta-gene set analysis of large numbers of gene expression datasets. The iterative algorithm extracts groups of phenotypes from multiple studies that are associated with similar gene sets. iBBiG does not require prior knowledge of the number or scale of clusters and allows discovery of clusters with diverse sizes
Author: Daniel Gusenleitner, Aedin Culhane
Maintainer: Aedin Culhane <aedin at jimmy.harvard.edu>
citation("iBBiG")):
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("iBBiG")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | Annotation, Clustering, GeneSetEnrichment, Software |
| Version | 1.57.0 |
| In Bioconductor since | BioC 2.10 (R-2.15) (14.5 years) |
| License | Artistic-2.0 |
| Depends | biclust |
| Imports | stats4, xtable, ade4 |
| System Requirements | |
| URL | http://bcb.dfci.harvard.edu/~aedin/publications/ |
See More
| Suggests | methods |
| 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 | |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/iBBiG |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/iBBiG |
| Package Short Url | https://bioconductor.org/packages/iBBiG/ |
| Package Downloads Report | Download Stats |