Package: ADaCGH2 2.47.0

Ramon Diaz-Uriarte

ADaCGH2: Analysis of big data from aCGH experiments using parallel computing and ff objects

Analysis and plotting of array CGH data. Allows usage of Circular Binary Segementation, wavelet-based smoothing (both as in Liu et al., and HaarSeg as in Ben-Yaacov and Eldar), HMM, GLAD, CGHseg. Most computations are parallelized (either via forking or with clusters, including MPI and sockets clusters) and use ff for storing data.

Authors:Ramon Diaz-Uriarte <[email protected]> and Oscar M. Rueda <[email protected]>. Wavelet-based aCGH smoothing code from Li Hsu <[email protected]> and Douglas Grove <[email protected]>. Imagemap code from Barry Rowlingson <[email protected]>. HaarSeg code from Erez Ben-Yaacov; downloaded from <http://www.ee.technion.ac.il/people/YoninaEldar/Info/software/HaarSeg.htm>. Code from ffbase <https://github.com/edwindj/ffbase> by Edwin de Jonge <[email protected]>, Jan Wijffels, Jan van der Laan.

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ADaCGH2.pdf |ADaCGH2.html✨
ADaCGH2/json (API)
NEWS

# Install 'ADaCGH2' in R:

install.packages('ADaCGH2', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rdiaz02/adacgh2/issues

Datasets:

inputEx - A fictitious aCGH data set
inputEx-sp - A fictitious aCGH data set

On BioConductor:ADaCGH2-2.47.0(bioc 3.21)ADaCGH2-2.46.0(bioc 3.20)

microarray copynumbervariants

3.48 score 3 scripts 382 downloads 10 exports 90 dependencies

Last updated 2 months agofrom:a79cd26355. Checks:OK: 5 NOTE: 4. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 29 2024
R-4.5-win-x86_64	OK	Nov 29 2024
R-4.5-linux-x86_64	OK	Nov 29 2024
R-4.4-win-x86_64	OK	Nov 29 2024
R-4.4-mac-x86_64	NOTE	Nov 29 2024
R-4.4-mac-aarch64	NOTE	Nov 29 2024
R-4.3-win-x86_64	OK	Nov 29 2024
R-4.3-mac-x86_64	NOTE	Nov 29 2024
R-4.3-mac-aarch64	NOTE	Nov 29 2024

Exports:cutFile inputToADaCGH outputToCGHregions pChromPlot pSegmentCGHseg pSegmentDNAcopy pSegmentGLAD pSegmentHaarSeg pSegmentHMM pSegmentWavelets

Dependencies:aCGH affy affyio annotate AnnotationDbi askpass aws awsMethods Biobase BiocGenerics BiocManager Biostrings bit bit64 blob cachem cli cluster colorspace cpp11 crayon curl DBI DNAcopy fansi farver fastmap ff genefilter generics GenomeInfoDb GenomeInfoDbData ggplot2 GLAD glue gsl gtable httr IRanges isoband jsonlite KEGGREST labeling lattice lifecycle limma magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime multitaper multtest munsell nlme openssl pillar pixmap pkgconfig plogr png preprocessCore R6 RColorBrewer rlang RSQLite S4Vectors sandwich scales statmod strucchange survival sys tibble tilingArray UCSC.utils utf8 vctrs viridisLite vsn waveslim withr XML xtable XVector zlibbioc zoo

ADaCGH2 Overview

Rendered fromADaCGH2.Rnwusingutils::Sweaveon Nov 29 2024.

Last update: 2024-02-05
Started: 2013-05-30

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Cut a file and return individual columns	cutFile
A fictitious aCGH data set	inputEx inputEx-sp inputEx.nona
Convert CGH data to ff or RAM objects for use with ADaCGH2	inputToADaCGH
ADaCGH2 output as input to CGHregions	outputToCGHregions
Segment plots for aCGH as PNG	pChromPlot
Parallelized/"unified" versions of several aCGH segementation algorithms/methods	pSegment pSegmentCGHseg pSegmentDNAcopy pSegmentGLAD pSegmentHaarSeg pSegmentHMM pSegmentWavelets