biovizBase v1.20.0

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.

Functions in biovizBase

Name Description
GCcontent GC content computation for BSgenome
isIdeogram Ideogram checking
biovizBase-package biovizBase is a package which provides utilities and color scheme...
splitByFacets split a GRanges by formula
getIdeoGR Get ideogram information
getBioColor Color scheme getter for biological data
parseArgsForAes Utils for parsing (un)evaluated arguments
ideo ideogram without cytoband information
isSimpleIdeogram Simple ideogram checking
getScale Get scale information from a GRanges
isMatchedWithModel Utils for Splicing Summary
crunch Fetching GRanges from various data source
plotColorLegend Show colors
showColor Show colors
strip_formula_dots strip dots around a formula variables
crc1.GeRL crc1.GeRL
pileupAsGRanges Summarize reads for certain region
getIdeogram Get ideogram.
getXScale get x scale breaks and labels
subsetArgsByFormals Subset list of arguments by functions
addStepping-method Adding disjoint levels to a GenomicRanges object
getYLab-method parse x and y label information from a specific object
transformGRangesForEvenSpace Transform GRanges with New Coordinates
shrinkageFun-method Shrinkage function
getGaps get gaps for a stepping transformed GRanges object
estimateCoverage Estimation of Coverage
CRC CRC
mold mold data into data.frame
darned_hg19_subset500 Subset of RNA editing sites in hg19...
getFormalNames Get formals from functions
hg19IdeogramCyto Hg19 ideogram with cytoband information...
ideoCyto ideogram with cytoband information
containLetters Checking if string contains letters or not
flatGrl Transform GRangesList to GRanges
pileupGRangesAsVariantTable Mismatch summary
maxGap-method Estimated max gaps
genesymbol Gene symbols with position...
hg19Ideogram Hg19 ideogram without cytoband information...
colorBlindSafePal Color blind safe palette generator
transformToGenome Transform GRanges to different coordinates and layout
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Details

License Artistic-2.0
LazyLoad Yes
Collate utils.R color.R AllGenerics.R crunch-method.R mold-method.R addStepping-method.R getFragLength-method.R shrinkageFun-method.R maxGap-method.R spliceSummary-method.R ideogram.R pileup.R coverage.R labs.R original.R transform.R facets-method.R aes.R scale.R zzz.R biovizBase-package.R
biocViews Infrastructure, Visualization, Preprocessing

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