Package: rCGH 1.37.0

Frederic Commo

rCGH: Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data

A comprehensive pipeline for analyzing and interactively visualizing genomic profiles generated through commercial or custom aCGH arrays. As inputs, rCGH supports Agilent dual-color Feature Extraction files (.txt), from 44 to 400K, Affymetrix SNP6.0 and cytoScanHD probeset.txt, cychp.txt, and cnchp.txt files exported from ChAS or Affymetrix Power Tools. rCGH also supports custom arrays, provided data complies with the expected format. This package takes over all the steps required for individual genomic profiles analysis, from reading files to profiles segmentation and gene annotations. This package also provides several visualization functions (static or interactive) which facilitate individual profiles interpretation. Input files can be in compressed format, e.g. .bz2 or .gz.

Authors:Frederic Commo [aut, cre]

rCGH_1.37.0.tar.gz
rCGH_1.37.0.zip(r-4.5)rCGH_1.37.0.zip(r-4.4)rCGH_1.37.0.zip(r-4.3)
rCGH_1.37.0.tgz(r-4.4-any)rCGH_1.37.0.tgz(r-4.3-any)
rCGH_1.37.0.tar.gz(r-4.5-noble)rCGH_1.37.0.tar.gz(r-4.4-noble)
rCGH_1.37.0.tgz(r-4.4-emscripten)rCGH_1.37.0.tgz(r-4.3-emscripten)
rCGH.pdf |rCGH.html✨
rCGH/json (API)
NEWS

# Install 'rCGH' in R:
install.packages('rCGH', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/fredcommo/rcgh/issues

Datasets:
  • agilentDB - ACGH Agilent Probes GC Fraction
  • hg18 - Hg18 Chromosome Lengths and Centromere Locations
  • hg19 - Hg19 Chromosome Lengths and Centromere Locations
  • hg38 - Hg38 Chromosome Lengths and Centromere Locations

On BioConductor:rCGH-1.37.0(bioc 3.21)rCGH-1.36.0(bioc 3.20)

acghcopynumbervariationpreprocessingfeatureextraction

5.10 score 4 stars 1 packages 26 scripts 268 downloads 2 mentions 20 exports 122 dependencies

Last updated 2 months agofrom:f2bf7cc026. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 06 2024
R-4.5-winNOTEDec 06 2024
R-4.5-linuxNOTEDec 06 2024
R-4.4-winNOTEDec 06 2024
R-4.4-macNOTEDec 06 2024
R-4.3-winNOTEDec 06 2024
R-4.3-macNOTEDec 06 2024

Exports:adjustSignalbyGeneTableEMnormalizegetCNsetgetInfogetParamgetSegTablemultiplotplotDensityplotLOHplotProfilereadAffyCytoScanreadAffyOncoScanreadAffySNP6readAgilentreadGenericrecenter<-segmentCGHsetInfo<-view

Dependencies:abindaCGHaffyaffyioAnnotationDbiaskpassbase64encBHBiobaseBiocGenericsBiocIOBiocManagerBiocParallelBiostringsbitbit64bitopsblobbslibcachemcliclustercodetoolscolorspacecommonmarkcpp11crayoncurlDBIDelayedArraydigestDNAcopyfansifarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegtablehtmltoolshttpuvhttrIRangesisobandjquerylibjsonliteKEGGRESTlabelinglambda.rlaterlatticelifecyclelimmamagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemgcvmimemulttestmunsellnlmeopensslorg.Hs.eg.dbpillarpkgconfigplogrplyrpngpreprocessCorepromisesR6rappdirsRColorBrewerRcppRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssassscalesshinysnowsourcetoolsSparseArraystatmodSummarizedExperimentsurvivalsystibbleTxDb.Hsapiens.UCSC.hg18.knownGeneTxDb.Hsapiens.UCSC.hg19.knownGeneTxDb.Hsapiens.UCSC.hg38.knownGeneUCSC.utilsutf8vctrsviridisLitewithrXMLxtableXVectoryamlzlibbioc

using rCGH package

Rendered fromrCGH.Rnwusingknitr::knitron Dec 06 2024.

Last update: 2017-11-30
Started: 2015-07-09

Readme and manuals

Help Manual

Help pageTopics
Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH DatarCGH-package rCGH
Array-based CGH PreprocessingadjustSignal adjustSignal,rCGH-method adjustSignal-methods
aCGH Agilent Probes GC FractionagilentDB
'"rCGH"' Accessor FunctionsAccessors AllAccessors getCNset getCNset,rCGH-method getCNset-methods getInfo getInfo,rCGH-method getInfo-methods getParam getParam,rCGH-method getParam-methods getSegTable getSegTable,rCGH-method getSegTable-methods
Converting a Segmentation Table Into a By-Gene TablebyGeneTable
Genomic Profile CentralizationEMnormalize EMnormalize,rCGH-method EMnormalize-methods
Hg18 Chromosome Lengths and Centromere Locationshg18
Hg19 Chromosome Lengths and Centromere Locationshg19
Hg38 Chromosome Lengths and Centromere Locationshg38
Static Genomic Profile and LOH Visualizationmultiplot multiplot,rCGH-method multiplot-methods
Visualizing the Log2Ratios Density and Centralization DecisionplotDensity plotDensity,rCGH-method plotDensity-methods
Allelic Differences VisualizationplotLOH plotLOH,rCGH-method plotLOH-methods
Static Genomic Profile VisualizationplotProfile plotProfile,rCGH-method plotProfile-methods
Class '"rCGH-Agilent"'rCGH-Agilent-class
Class '"rCGH"'rCGH-class
Class '"rCGH-cytoScan"'rCGH-cytoScan-class
Class '"rCGH-generic"'rCGH-generic-class
Class '"rCGH-oncoScan"'rCGH-oncoScan-class
Class '"rCGH-SNP6"'rCGH-SNP6-class
Affymetrix CytoScanHD '"rCGH-cytoScan"' ConstructorreadAffyCytoScan
Affymetrix OncoScan '"rCGH-oncoScan"' ConstructorreadAffyOncoScan
Affymetrix SNP6 '"rCGH-SNP6"' ConstructorreadAffySNP6
Agilent Dual-Color Hybridization '"rCGH-Agilent"' Constructor.readAgilent
Generic rCGH object '"rCGH-generic"' ConstructorreadGeneric
Recentering a Genomic Profilerecenter recenter<- recenter<-,rCGH-method recenter<--methods
Genomic Profile SegmentationsegmentCGH segmentCGH,rCGH-method segmentCGH-methods
Adding Information In An Object Of Class '"rCGH"'setInfo setInfo<- setInfo<-,rCGH-method setInfo<--methods
'show' '"rCGH"'show,rCGH-method show-methods
Interactive Genomic Profile Visualizationview view,rCGH-method view-methods