biovizBase: Basic graphic utilities for visualization of genomic data.

The biovizBase package is designed to provide a set of utilities, color schemes and conventions for genomic data. It serves as the base for various high-level packages for biological data visualization. This saves development effort and encourages consistency.

AuthorTengfei Yin [aut], Michael Lawrence [aut, ths, cre], Dianne Cook [aut, ths], Johannes Rainer [ctb]
Date of publicationNone
MaintainerMichael Lawrence <lawrence.michael@gene.com>
LicenseArtistic-2.0
Version1.22.0

View on Bioconductor

Man pages

addStepping-method: Adding disjoint levels to a GenomicRanges object

aes-utils: Utils for parsing (un)evaluated arguments

biovizBase-package: biovizBase is a package which provides utilities and color...

colorBlindSafePal: Color blind safe palette generator

containLetters: Checking if string contains letters or not

CRC: CRC

crc1.GeRL: crc1.GeRL

crunch-method: Fetching GRanges from various data source

darned_hg19_subset500: Subset of RNA editing sites in hg19...

estimateCoverage-method: Estimation of Coverage

flatGrl: Transform GRangesList to GRanges

GCcontent: GC content computation for BSgenome

genesymbol: Gene symbols with position...

getBioColor: Color scheme getter for biological data

getFormalNames: Get formals from functions

getGaps: get gaps for a stepping transformed GRanges object

getIdeoGR: Get ideogram information

getIdeogram: Get ideogram.

getScale: Get scale information from a GRanges

hg19Ideogram: Hg19 ideogram without cytoband information...

hg19IdeogramCyto: Hg19 ideogram with cytoband information...

ideo: ideogram without cytoband information

ideoCyto: ideogram with cytoband information

isIdeogram: Ideogram checking

isMatchedWithModel: Utils for Splicing Summary

isSimpleIdeogram: Simple ideogram checking

labs: parse x and y label information from a specific object

maxGap-method: Estimated max gaps

mold-method: mold data into data.frame

pileupAsGRanges: Summarize reads for certain region

pileupGRangesAsVariantTable: Mismatch summary

plotColorLegend: Show colors

scale: get x scale breaks and labels

showColor: Show colors

shrinkageFun-method: Shrinkage function

splitByFacets-method: split a GRanges by formula

strip_formula_dots: strip dots around a formula variables

subsetArgsByFormals: Subset list of arguments by functions

transform: Transform GRanges to different coordinates and layout

transformGRangesForEvenSpace: Transform GRanges with New Coordinates

Files in this package

biovizBase/DESCRIPTION
biovizBase/NAMESPACE
biovizBase/NEWS
biovizBase/R
biovizBase/R/AllGenerics.R biovizBase/R/addStepping-method.R biovizBase/R/aes.R biovizBase/R/biovizBase-package.R biovizBase/R/color.R biovizBase/R/coverage.R biovizBase/R/crunch-method.R biovizBase/R/facets-method.R biovizBase/R/getFragLength-method.R biovizBase/R/ideogram.R biovizBase/R/labs.R biovizBase/R/maxGap-method.R biovizBase/R/mold-method.R biovizBase/R/original.R biovizBase/R/pileup.R biovizBase/R/scale.R biovizBase/R/shrinkageFun-method.R biovizBase/R/spliceSummary-method.R biovizBase/R/transform.R biovizBase/R/utils.R biovizBase/R/zzz.R
biovizBase/build
biovizBase/build/vignette.rds
biovizBase/data
biovizBase/data/CRC.rda
biovizBase/data/crc1.GeRL.rda
biovizBase/data/darned_hg19_subset500.rda
biovizBase/data/genesymbol.rda
biovizBase/data/hg19Ideogram.rda
biovizBase/data/hg19IdeogramCyto.rda
biovizBase/data/ideo.rda
biovizBase/data/ideoCyto.rda
biovizBase/inst
biovizBase/inst/doc
biovizBase/inst/doc/intro.R
biovizBase/inst/doc/intro.Rnw
biovizBase/inst/doc/intro.pdf
biovizBase/inst/examples
biovizBase/inst/examples/color.R
biovizBase/inst/examples/data-gen.R
biovizBase/inst/examples/test.R
biovizBase/inst/extdata
biovizBase/inst/extdata/17-1409-CEU-brca1.vcf.bgz
biovizBase/inst/extdata/17-1409-CEU-brca1.vcf.bgz.tbi
biovizBase/inst/extdata/SRR027894subRBM17.bam
biovizBase/inst/extdata/SRR027894subRBM17.bam.bai
biovizBase/inst/extdata/crc-rearrangment.csv
biovizBase/inst/extdata/crc1-missense.csv
biovizBase/inst/extdata/plink.assoc.sub.txt
biovizBase/inst/extdata/wg-brca1.sorted.bam
biovizBase/inst/extdata/wg-brca1.sorted.bam.bai
biovizBase/inst/unitTests
biovizBase/inst/unitTests/test_ensdb.R
biovizBase/man
biovizBase/man/CRC.Rd biovizBase/man/GCcontent.Rd biovizBase/man/addStepping-method.Rd biovizBase/man/aes-utils.Rd biovizBase/man/biovizBase-package.Rd biovizBase/man/colorBlindSafePal.Rd biovizBase/man/containLetters.Rd biovizBase/man/crc1.GeRL.Rd biovizBase/man/crunch-method.Rd biovizBase/man/darned_hg19_subset500.Rd biovizBase/man/estimateCoverage-method.Rd biovizBase/man/flatGrl.Rd biovizBase/man/genesymbol.Rd biovizBase/man/getBioColor.Rd biovizBase/man/getFormalNames.Rd biovizBase/man/getGaps.Rd biovizBase/man/getIdeoGR.Rd biovizBase/man/getIdeogram.Rd biovizBase/man/getScale.Rd biovizBase/man/hg19Ideogram.Rd biovizBase/man/hg19IdeogramCyto.Rd biovizBase/man/ideo.Rd biovizBase/man/ideoCyto.Rd biovizBase/man/isIdeogram.Rd biovizBase/man/isMatchedWithModel.Rd biovizBase/man/isSimpleIdeogram.Rd biovizBase/man/labs.Rd biovizBase/man/maxGap-method.Rd biovizBase/man/mold-method.Rd biovizBase/man/pileupAsGRanges.Rd biovizBase/man/pileupGRangesAsVariantTable.Rd biovizBase/man/plotColorLegend.Rd biovizBase/man/scale.Rd biovizBase/man/showColor.Rd biovizBase/man/shrinkageFun-method.Rd biovizBase/man/splitByFacets-method.Rd biovizBase/man/strip_formula_dots.Rd biovizBase/man/subsetArgsByFormals.Rd biovizBase/man/transform.Rd biovizBase/man/transformGRangesForEvenSpace.Rd
biovizBase/src
biovizBase/src/R_init_biovizBase.c
biovizBase/src/bin_offsets.c
biovizBase/src/bin_offsets.h
biovizBase/tests
biovizBase/tests/runTests.R
biovizBase/vignettes
biovizBase/vignettes/intro-shrink-single.pdf
biovizBase/vignettes/intro-shrinkageFun.pdf
biovizBase/vignettes/intro.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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