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biovizBase (version 1.20.0)

Basic graphic utilities for visualization of genomic data.

Description

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.

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Version

Version

1.20.0

License

Artistic-2.0

Maintainer

Michael Lawrence

Last Published

February 15th, 2017

Functions in biovizBase (1.20.0)

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