Package: biomvRCNS 1.47.0

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_1.47.0.tar.gz
biomvRCNS_1.47.0.zip(r-4.5)biomvRCNS_1.47.0.zip(r-4.4)biomvRCNS_1.47.0.zip(r-4.3)
biomvRCNS_1.47.0.tgz(r-4.4-x86_64)biomvRCNS_1.47.0.tgz(r-4.4-arm64)biomvRCNS_1.47.0.tgz(r-4.3-x86_64)biomvRCNS_1.47.0.tgz(r-4.3-arm64)
biomvRCNS_1.47.0.tar.gz(r-4.5-noble)biomvRCNS_1.47.0.tar.gz(r-4.4-noble)
biomvRCNS_1.47.0.tgz(r-4.4-emscripten)biomvRCNS_1.47.0.tgz(r-4.3-emscripten)
biomvRCNS.pdf |biomvRCNS.html✨
biomvRCNS/json (API)
NEWS

# 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-1.47.0(bioc 3.21)biomvRCNS-1.46.0(bioc 3.20)

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

3.48 score 2 scripts 334 downloads 1 mentions 12 exports 148 dependencies

Last updated 2 months agofrom:de5ca1593e. Checks:OK: 1 NOTE: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 21 2024
R-4.5-win-x86_64	NOTE	Nov 21 2024
R-4.5-linux-x86_64	NOTE	Dec 21 2024
R-4.4-win-x86_64	NOTE	Nov 21 2024
R-4.4-mac-x86_64	NOTE	Dec 21 2024
R-4.4-mac-aarch64	NOTE	Dec 21 2024
R-4.3-win-x86_64	NOTE	Nov 21 2024
R-4.3-mac-x86_64	NOTE	Dec 21 2024
R-4.3-mac-aarch64	NOTE	Dec 21 2024

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

Dependencies:abind AnnotationDbi AnnotationFilter askpass backports base64enc BH Biobase BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem checkmate cli cluster codetools colorspace cpp11 crayon curl data.table DBI dbplyr DelayedArray deldir dichromat digest dplyr ensembldb evaluate fansi farver fastmap filelock fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData 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 mgcv mime munsell mvtnorm nlme nnet openssl pillar pkgconfig plogr png prettyunits progress ProtGenerics purrr R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl restfulr Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors sass scales snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite withr xfun XML xml2 XVector yaml zlibbioc

biomvRCNS package introduction

Rendered frombiomvRCNS.Rnwusingutils::Sweaveon Dec 21 2024.

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