Science Score: 13.0%
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Repository
UniBic Biclustering algorithm for R
Basic Info
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- Stars: 4
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Metadata Files
README.md
runibic: UniBic biclustering algorithm for R
This package contains implementation of UniBic biclustering algorithm for gene expression data [Wang2016] The algorithm tries to locate trend-preserving biclusters within complex and noisy data.
Functions
This package provides the following main functions:
* BCUnibic/runibic - parallel UniBic for continuous data
* BCUnibicD - parallel UniBic for discrete data
The package provides some additional functions:
* pairwiseLCS - calculates Longest Common Subsequence (LCS) between two vectors
* calculateLCS - calculates LCSes between all pairs of the input dataset
* backtrackLCS - recovers LCS from the dynamic programming matrix
* cluster - main part of UniBic algorithm (biclusters seeding and expanding)
* unisort - returns matrix of indexes based on the increasing order in each row
* discretize - performs discretization using Fibonacci heap (sorting method used originally in UniBic) or standard sorting
Installation
The package may be installed as follows:
r
install.packages("devtools")
devtools::install_github("athril/runibic")
Example
Gene expression dataset
This example presents how to use runibic package on gene expression dataset:
r
library(runibic)
library(biclust)
data(BicatYeast)
res <- biclust(method=BCUnibic(),BicatYeast)
drawHeatmap(BicatYeast, res, 1)
parallelCoordinates(BicatYeast,res,1)
Summarized experiment
This example presents how to use runibic package on SummarizedExperiment:
r
library(runibic)
library(biclust)
library(SummarizedExperiment)
data(airway, package="airway")
se <- airway[1:20,]
res<- runibic(se)
parallelCoordinates(assays(se)[[1]], res[[1]], 2)
Tutorial
Please check runibic tutorial
Citation
For the original sequential version of the UniBic please use the following citation:
Zhenjia Wang, Guojun Li, Robert W. Robinson, Xiuzhen Huang UniBic: Sequential row-based biclustering algorithm for analysis of gene expression data Scientific Reports 6, 2016; 23466, doi: https://doi:10.1038/srep23466
If you use in your work this package with parallel version of UniBic please use the following citation:
Patryk Orzechowski, Artur Pańszczyk, Xiuzhen Huang Jason H. Moore: runibic: a Bioconductor package for parallel row-based biclustering of gene expression data bioRxiv, 2017; 210682, doi: https://doi.org/10.1101/210682
BibTex entry:
@article{orzechowski2018runibic,
author = {Orzechowski, Patryk and Pańszczyk, Artur and Huang, Xiuzhen and Moore, Jason H},
title = {runibic: a Bioconductor package for parallel row-based biclustering of gene expression data},
journal = {Bioinformatics},
volume = {},
number = {},
pages = {bty512},
year = {2018},
doi = {10.1093/bioinformatics/bty512},
URL = {http://dx.doi.org/10.1093/bioinformatics/bty512},
eprint = {/oup/backfile/content_public/journal/bioinformatics/pap/10.1093_bioinformatics_bty512/4/bty512.pdf}
}
References
- [Wang2016] Wang, Zhenjia, et al. "UniBic: Sequential row-based biclustering algorithm for analysis of gene expression data." Scientific reports 6 (2016): 23466.
Owner
- Name: Patryk Orzechowski
- Login: athril
- Kind: user
- Location: Philadelphia, USA
- Company: University of Pennsylvania
- Repositories: 26
- Profile: https://github.com/athril
Data Scientist @ University of Pennsylvania
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| Name | Commits | |
|---|---|---|
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| Hervé Pagès | h****s@f****g | 2 |
| vobencha | v****n@r****g | 2 |
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- Total packages: 1
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Total downloads:
- bioconductor 15,145 total
- Total dependent packages: 1
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- Total versions: 5
- Total maintainers: 1
bioconductor.org: runibic
runibic: row-based biclustering algorithm for analysis of gene expression data in R
- Homepage: http://github.com/athril/runibic
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/runibic/inst/doc/runibic.pdf
- License: MIT + file LICENSE
-
Latest release: 1.30.0
published over 1 year ago
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Maintainers (1)
Dependencies
- R >= 3.4.0 depends
- SummarizedExperiment * depends
- biclust * depends
- Rcpp >= 0.12.12 imports
- methods * imports
- testthat * imports
- GEOquery * suggests
- QUBIC * suggests
- affy * suggests
- airway * suggests
- knitr * suggests
- rmarkdown * suggests