Analysis of Transposable Elements

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Documentation for package ‘atena’ version 1.10.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
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atena-package	atena: analysis of transposable elements in R and Bioconductor
annotaTEs	Get RepeatMasker UCSC annotations
annotateTEsGetters	Getter functions of TE classes from parsed RepeatMasker annotations.
atena	atena: analysis of transposable elements in R and Bioconductor
atenaParam	atena parameter class
atenaParam-class	atena parameter class
ERVmapParam	ERVmap parameter class
ERVmapParam-class	ERVmap parameter class
features-method	QuantifyParam parameter class
getDNAtransposons	Getter functions of TE classes from parsed RepeatMasker annotations.
getLINEs	Getter functions of TE classes from parsed RepeatMasker annotations.
getLTRs	Getter functions of TE classes from parsed RepeatMasker annotations.
getSINEs	Getter functions of TE classes from parsed RepeatMasker annotations.
OneCodeToFindThemAll	OneCodeToFindThemAll parser of RepeatMasker annotations
ovIntersectionStrict	Pre-defined overlapping mode functions
ovUnion	Pre-defined overlapping mode functions
path-method	QuantifyParam parameter class
qtex	Quantify transposable element expression
qtex-method	Quantify transposable element expression
QuantifyParam-class	QuantifyParam parameter class
rmskatenaparser	atena annotation parser of RepeatMasker annotations
rmskbasicparser	Parser of RepeatMasker annotations
rmskidentity	Identity function for parsefun
show-method	ERVmap parameter class
show-method	TEtranscripts parameter class
show-method	Telescope parameter class
show-method	atena parameter class
TelescopeParam	Telescope parameter class
TelescopeParam-class	Telescope parameter class
TEtranscriptsParam	TEtranscripts parameter class
TEtranscriptsParam-class	TEtranscripts parameter class