Package: MCbiclust 1.29.0

Robert Bentham

MCbiclust: Massive correlating biclusters for gene expression data and associated methods

Custom made algorithm and associated methods for finding, visualising and analysing biclusters in large gene expression data sets. Algorithm is based on with a supplied gene set of size n, finding the maximum strength correlation matrix containing m samples from the data set.

Authors:Robert Bentham

MCbiclust_1.29.0.tar.gz
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MCbiclust.pdf |MCbiclust.html✨
MCbiclust/json (API)

# Install 'MCbiclust' in R:

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

Datasets:

CCLE_samples - Clinical information for CCLE data
CCLE_small - Subset of expression levels of CCLE data
Mitochondrial_genes - List of known mitochondrial genes

On BioConductor:MCbiclust-1.29.0(bioc 3.20)MCbiclust-1.28.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

14 exports 0.91 score 133 dependencies 1 mentions

Last updated 2 months agofrom:1a3df25ffc

Exports:CorScoreCalc CVEval CVPlot FindSeed ForkClassifier GOEnrichmentAnalysis HclustGenesHiCor MultiSampleSortPrep PC1Align PC1VecFun PointScoreCalc SampleSort SilhouetteClustGroups ThresholdBic

Dependencies:AnnotationDbi askpass backports base64enc BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 blob broom broom.helpers bslib cachem checkmate cli clipr cluster codetools colorspace cpp11 crayon curl data.table DBI digest doParallel dplyr dynamicTreeCut evaluate fansi farver fastcluster fastmap fontawesome forcats foreach foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GGally ggplot2 ggstats glue GO.db gridExtra gtable haven highr Hmisc hms htmlTable htmltools htmlwidgets httr impute IRanges isoband iterators jquerylib jsonlite KEGGREST knitr labeling labelled lambda.r lattice lifecycle magrittr MASS Matrix matrixStats memoise mgcv mime munsell nlme nnet openssl org.Hs.eg.db patchwork pillar pkgconfig plogr plyr png preprocessCore prettyunits progress purrr R6 rappdirs RColorBrewer Rcpp readr rlang rmarkdown rpart RSQLite rstudioapi S4Vectors sass scales snow stringi stringr survival sys tibble tidyr tidyselect tinytex tzdb UCSC.utils utf8 vctrs viridis viridisLite vroom WGCNA withr xfun XVector yaml zlibbioc

Introduction to MCbiclust

Robert Bentham

Rendered fromMCbiclust_vignette.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2024-02-11
Started: 2016-08-17

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Clinical information for CCLE data	CCLE_samples
Subset of expression levels of CCLE data	CCLE_small
Calculate correlation score	CorScoreCalc
Method for the calculation of a correlation vector	CVEval
Make correlation vector plot	CVPlot
Find highly correlated seed of samples for gene expression matrix	FindSeed
Calculate gene set enrichment of correlation vector using Mann-Whitney test	GOEnrichmentAnalysis
Find the most highly correlated genes using hierarchical clustering	HclustGenesHiCor
MCbiclust: Massively Correlated biclustering	MCbiclust-package MCbiclust
List of known mitochondrial genes	Mitochondrial_genes
Calculate PC1 vector of found pattern	PC1VecFun
Calculate PointScore	PointScoreCalc
Methods for ordering samples	MultiSampleSortPrep SampleSort
Slihouette validation of correlation vector clusters	SilhouetteClustGroups
Methods for defining a bicluster	ForkClassifier PC1Align ThresholdBic