Package: runibic 1.29.0

Patryk Orzechowski

runibic: runibic: row-based biclustering algorithm for analysis of gene expression data in R

This package implements UbiBic algorithm in R. This biclustering algorithm for analysis of gene expression data was introduced by Zhenjia Wang et al. in 2016. It is currently considered the most promising biclustering method for identification of meaningful structures in complex and noisy data.

Authors:Patryk Orzechowski, Artur Pańszczyk

runibic_1.29.0.tar.gz
runibic_1.29.0.zip(r-4.5)runibic_1.29.0.zip(r-4.4)runibic_1.29.0.zip(r-4.3)

runibic_1.29.0.tar.gz(r-4.5-noble)runibic_1.29.0.tar.gz(r-4.4-noble)
runibic.pdf |runibic.html✨
runibic/json (API)
NEWS

# Install 'runibic' in R:

install.packages('runibic', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/athril/runibic/issues

Uses libs:

c++– GNU Standard C++ Library v3
openmp– GCC OpenMP (GOMP) support library

On BioConductor:runibic-1.29.0(bioc 3.21)runibic-1.28.0(bioc 3.20)

microarray clustering geneexpression sequencing coverage cpp openmp

5.20 score 4 stars 7 scripts 206 downloads 2 mentions 10 exports 81 dependencies

Last updated 3 months agofrom:c55baab949. Checks:1 OK, 4 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Dec 27 2024
R-4.5-win-x86_64	NOTE	Dec 30 2024
R-4.5-linux-x86_64	NOTE	Dec 27 2024
R-4.4-win-x86_64	NOTE	Dec 30 2024
R-4.3-win-x86_64	NOTE	Dec 31 2024

Exports:backtrackLCS BCUnibic BCUnibicD calculateLCS cluster pairwiseLCS runibic runiDiscretize set_runibic_params unisort

Dependencies:abind additivityTests askpass biclust Biobase BiocGenerics brio callr class cli colorspace cpp11 crayon curl DelayedArray desc diffobj digest dplyr evaluate fansi farver flexclust fs generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gtable httr IRanges isoband jsonlite labeling lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats mgcv mime modeltools munsell nlme openssl pillar pkgbuild pkgconfig pkgload praise processx ps purrr R6 RColorBrewer Rcpp rlang rprojroot S4Arrays S4Vectors scales SparseArray stringi stringr SummarizedExperiment sys testthat tibble tidyr tidyselect UCSC.utils utf8 vctrs viridisLite waldo withr XVector

runibic: UniBic in R Tutorial

Patryk Orzechowski, Artur Pańszczyk

Rendered fromrunibic.Rmdusingknitr::rmarkdownon Dec 27 2024.

Last update: 2018-09-20
Started: 2017-10-04

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Retrieving a Longest Common Subsequence between two integer vectors.	backtrackLCS
Class BCUnibic	BCUnibic-class
Class BCUnibicD	BCUnibicD-class
Calculate all Longest Common Subsequences between a matrix.	calculateLCS
Calculate biclusters from sorted list of LCS scores and row indices	cluster
Calculate a matrix of Longest Common Subsequence (LCS) between a pair of numeric vectors	pairwiseLCS
runibic: parallel row-based biclustering algorithm for analysis of gene expression data in R	runibic-package BCUnibic BCUnibicD runibic
Discretize an input matrix	runiDiscretize
Set the parameters for runibic algorithm	set_runibic_params
Computing the indexes of j-th smallest values of each row	unisort