# Analysis of Transposable Elements

## Documentation for package ‘atena’ version 1.11.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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