Package: biomvRCNS 1.53.0

Yang Du

biomvRCNS: Copy Number study and Segmentation for multivariate biological data

In this package, a Hidden Semi Markov Model (HSMM) and one homogeneous segmentation model are designed and implemented for segmentation genomic data, with the aim of assisting in transcripts detection using high throughput technology like RNA-seq or tiling array, and copy number analysis using aCGH or sequencing.

Authors:Yang Du

biomvRCNS_1.53.0.tar.gz
biomvRCNS_1.53.0.zip(r-4.7)biomvRCNS_1.53.0.zip(r-4.6)biomvRCNS_1.53.0.zip(r-4.5)
biomvRCNS_1.53.0.tgz(r-4.6-x86_64)biomvRCNS_1.53.0.tgz(r-4.6-arm64)biomvRCNS_1.53.0.tgz(r-4.5-x86_64)biomvRCNS_1.53.0.tgz(r-4.5-arm64)
biomvRCNS_1.53.0.tar.gz(r-4.7-arm64)biomvRCNS_1.53.0.tar.gz(r-4.7-x86_64)biomvRCNS_1.53.0.tar.gz(r-4.6-arm64)biomvRCNS_1.53.0.tar.gz(r-4.6-x86_64)
biomvRCNS_1.53.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
biomvRCNS/json (API)

# Install 'biomvRCNS' in R:

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

Datasets:

coriell - Array CGH data set of Coriell cell lines
encodeTP53 - Mapped RNA-seq data from ENCODE
variosm - Differential methylation data from sequencing

On BioConductor:biomvRCNS-1.53.0(bioc 3.24)biomvRCNS-1.52.0(bioc 3.23)

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

acgh copynumbervariation microarray sequencing visualization genetics

3.30 score 2 scripts 1 mentions 12 exports 144 dependencies

Last updated from:0f85d22a02. Checks:1 ERROR, 11 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	239
linux-devel-arm64	NOTE	403
linux-devel-x86_64	NOTE	496
source / vignettes	OK	605
linux-release-arm64	NOTE	452
linux-release-x86_64	NOTE	496
macos-release-arm64	NOTE	284
macos-release-x86_64	NOTE	504
macos-oldrel-arm64	NOTE	266
macos-oldrel-x86_64	NOTE	497
windows-devel	NOTE	411
windows-release	NOTE	392
windows-oldrel	NOTE	404
wasm-release	OK	180

Exports:biomvRGviz biomvRhsmm biomvRmgmr biomvRseg hsmmRun maxGapminRun regionSegAlphaNB regionSegCost show simSegData sojournAnno splitFarNeighbour

Dependencies:abind AnnotationDbi AnnotationFilter askpass backports base64enc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem checkmate cigarillo cli cluster codetools colorspace cpp11 crayon curl data.table DBI dbplyr DelayedArray deldir dichromat digest dplyr ensembldb evaluate farver fastmap filelock fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gridExtra gtable Gviz highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 interp IRanges isoband jpeg jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice latticeExtra lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mime mvtnorm nnet openssl pillar pkgconfig png prettyunits progress ProtGenerics purrr R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl restfulr Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors S7 sass scales Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex UCSC.utils utf8 VariantAnnotation vctrs viridisLite withr xfun XML xml2 XVector yaml

biomvRCNS package introduction

Rendered frombiomvRCNS.Rnwusingutils::Sweave

Last update: 2016-02-22
Started: 2013-10-20

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Class '"biomvRCNS"'	biomvRCNS-class plot,biomvRCNS,ANY-method show,biomvRCNS-method
Plot segmentation result using Gviz	biomvRGviz
Estimating the most likely state sequence using Hidden Semi Markov Model	biomvRhsmm
Batch process multiple sequences and samples using max-gap-min-run algorithm for 2 states segmentation	biomvRmgmr
Homogeneous segmentation of multi-sample genomic data	biomvRseg
Array CGH data set of Coriell cell lines	coriell
mapped RNA-seq data from ENCODE	encodeTP53
Estimating the most likely state sequence using Hidden Semi Markov Model	hsmmRun
Max-gap-min-run algorithm for 2 states segmentation	maxGapminRun
Estimate matrix of dispersion parameter alpha (size) used in 'regionSegCost' for negative binomial distributed 'x'.	regionSegAlphaNB
Regional segmentation cost matrix	regionSegCost
Simulate exemplary segmentation data.	simSegData
Estimate sojourn distribution parameters from posterior information like annotation data	sojournAnno
Split segments if long gaps exist between feature positions	splitFarNeighbour
Differential methylation data from sequencing	variosm