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.

Author
Tengfei Yin [aut], Michael Lawrence [aut, ths, cre], Dianne Cook [aut, ths], Johannes Rainer [ctb]
Date of publication
None
Maintainer
Michael Lawrence <lawrence.michael@gene.com>
License
Artistic-2.0
Version
1.22.0

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