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.

AuthorFrederic Commo [aut, cre]
Date of publicationNone
MaintainerFrederic Commo <frederic.commo@gustaveroussy.fr>
LicenseArtistic-2.0
Version1.4.0
https://github.com/fredcommo/rCGH

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Files in this package

rCGH/DESCRIPTION
rCGH/NAMESPACE
rCGH/NEWS
rCGH/R
rCGH/R/AllClasses.R rCGH/R/AllGenerics.R rCGH/R/AllHelperFunctions.R rCGH/R/AllMethods.R rCGH/R/AllSetters.R rCGH/R/buildData.R rCGH/R/plotFunctions.R rCGH/R/zzz.R
rCGH/build
rCGH/build/vignette.rds
rCGH/data
rCGH/data/agilentDB_400K_GC.rda
rCGH/data/datalist
rCGH/data/hg18.rda
rCGH/data/hg19.rda
rCGH/data/hg38.rda
rCGH/inst
rCGH/inst/doc
rCGH/inst/doc/rCGH.R
rCGH/inst/doc/rCGH.Rnw
rCGH/inst/doc/rCGH.pdf
rCGH/inst/extdata
rCGH/inst/extdata/Affy_cytoScan.cyhd.CN5.CNCHP.txt.bz2
rCGH/inst/extdata/Affy_snp6_cnchp.txt.bz2
rCGH/inst/extdata/Agilent4x180K.txt.bz2
rCGH/inst/extdata/generic.txt.bz2
rCGH/inst/extdata/oncoscan.tsv.bz2
rCGH/inst/shinyProfile
rCGH/inst/shinyProfile/data
rCGH/inst/shinyProfile/data/empty.txt
rCGH/inst/shinyProfile/helpers.R
rCGH/inst/shinyProfile/server.R
rCGH/inst/shinyProfile/ui.R
rCGH/inst/shinyProfile/www
rCGH/inst/shinyProfile/www/style.css
rCGH/inst/unitTests
rCGH/inst/unitTests/test_rCGH.R
rCGH/man
rCGH/man/AllAccessors.Rd rCGH/man/EMnormalize.Rd rCGH/man/adjustSignal.Rd rCGH/man/agilentDB.Rd rCGH/man/byGeneTable.Rd rCGH/man/hg18.Rd rCGH/man/hg19.Rd rCGH/man/hg38.Rd rCGH/man/multiplot.Rd rCGH/man/plotDensity.Rd rCGH/man/plotLOH.Rd rCGH/man/plotProfile.Rd rCGH/man/rCGH-Agilent-class.Rd rCGH/man/rCGH-SNP6-class.Rd rCGH/man/rCGH-class.Rd rCGH/man/rCGH-cytoScan-class.Rd rCGH/man/rCGH-generic-class.Rd rCGH/man/rCGH-oncoScan-class.Rd rCGH/man/rCGH-package.Rd rCGH/man/readAffyCytoScan.Rd rCGH/man/readAffyOncoScan.Rd rCGH/man/readAffySNP6.Rd rCGH/man/readAgilent.Rd rCGH/man/readGeneric.Rd rCGH/man/recenter.Rd rCGH/man/segmentCGH.Rd rCGH/man/setInfo.Rd rCGH/man/show-methods.Rd rCGH/man/view.Rd
rCGH/tests
rCGH/tests/runTests.R
rCGH/vignettes
rCGH/vignettes/rCGH.Rnw
rCGH/vignettes/view.png
rCGH/vignettes/workflowOverview.pdf

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