Package: ADaCGH2 2.50.0
Ramon Diaz-Uriarte
ADaCGH2: Analysis of big data from aCGH experiments using parallelcomputing and ff objects
Analysis and plotting of array CGH data. Allows usage ofCircular Binary Segementation, wavelet-based smoothing (both asin Liu et al., and HaarSeg as in Ben-Yaacov and Eldar), HMM,GLAD, CGHseg. Most computations are parallelized (either viaforking 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 LiHsu <[email protected]> and Douglas Grove <[email protected]>.Imagemap code from Barry Rowlingson<[email protected]>. HaarSeg code from ErezBen-Yaacov; downloaded from<http://www.ee.technion.ac.il/people/YoninaEldar/Info/software/HaarSeg.htm>.Code from ffbase <https://github.com/edwindj/ffbase> by Edwinde Jonge <[email protected]>, Jan Wijffels, Jan van derLaan.
ADaCGH2_2.50.0.tar.gz
ADaCGH2_2.50.0.zip(r-4.6)ADaCGH2_2.50.0.zip(r-4.5)ADaCGH2_2.50.0.zip(r-4.4)
ADaCGH2_2.50.0.tgz(r-4.6-x86_64)ADaCGH2_2.50.0.tgz(r-4.6-arm64)ADaCGH2_2.50.0.tgz(r-4.5-x86_64)ADaCGH2_2.50.0.tgz(r-4.5-arm64)
ADaCGH2_2.50.0.tar.gz(r-4.6-arm64)ADaCGH2_2.50.0.tar.gz(r-4.6-x86_64)ADaCGH2_2.50.0.tar.gz(r-4.5-arm64)ADaCGH2_2.50.0.tar.gz(r-4.5-x86_64)
ADaCGH2_2.50.0.tgz(r-4.5-emscripten)
ADaCGH2.pdf |ADaCGH2.html✨
ADaCGH2/json (API)
NEWS
| # Install 'ADaCGH2' in R: |
| install.packages('ADaCGH2', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/rdiaz02/adacgh2/issues
- inputEx - A fictitious aCGH data set
- inputEx-sp - A fictitious aCGH data set
On BioConductor:ADaCGH2-2.51.0(bioc 3.23)ADaCGH2-2.50.0(bioc 3.22)
3.60 score 3 scripts 467 downloads 10 exports 75 dependencies
Last updated from:62d279406d (on RELEASE_3_22). Checks:1 ERROR, 13 OK. Indexed: no.
| Target | Result | Total time | Artifact |
|---|---|---|---|
| bioc-checks | ERROR | 169 | |
| linux-devel-arm64 | OK | 265 | |
| linux-devel-x86_64 | OK | 340 | |
| source / vignettes | OK | 332 | |
| linux-release-arm64 | OK | 284 | |
| linux-release-x86_64 | OK | 301 | |
| macos-devel-arm64 | OK | 333 | |
| macos-devel-x86_64 | OK | 381 | |
| macos-release-arm64 | OK | 223 | |
| macos-release-x86_64 | OK | 438 | |
| windows-devel | OK | 226 | |
| windows-release | OK | 220 | |
| windows-oldrel | OK | 256 | |
| wasm-release | OK | 133 |
Exports:cutFileinputToADaCGHoutputToCGHregionspChromPlotpSegmentCGHsegpSegmentDNAcopypSegmentGLADpSegmentHaarSegpSegmentHMMpSegmentWavelets
Dependencies:aCGHaffyaffyioannotateAnnotationDbiaskpassBiobaseBiocGenericsBiocManagerBiostringsbitbit64blobcachemcliclustercpp11crayoncurlDBIDNAcopyfarverfastmapffgenefiltergenericsggplot2gluegtablehttrIRangesisobandjsonliteKEGGRESTlabelinglatticelifecyclelimmaMASSMatrixMatrixGenericsmatrixStatsmemoisemimemultitapermulttestopensslpixmappkgconfigplogrpngpreprocessCoreR6RColorBrewerrlangRSQLiteS4VectorsS7sandwichscalesSeqinfostatmodstrucchangesurvivalsystilingArrayvctrsviridisLitevsnwaveslimwithrXMLxtableXVectorzoo
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 |
