# Analysis of Transposable Elements

## Documentation for package ‘atena’ version 1.8.0

- 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
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 | Atena parameter class
features-method | Atena parameter class
getDNAtransposons | Getter of DNA class TEs from parsed RepeatMasker annotations
getLINEs | Getter of LINE class TEs from parsed RepeatMasker annotations
getLTRs | Getter of LTR class TEs from parsed RepeatMasker annotations
getSINEs | Getter of SINE class TEs from parsed RepeatMasker annotations
OneCodeToFindThemAll | OneCodeToFindThemAll parser of RepeatMasker annotations
ovIntersectionStrict | Pre-defined overlapping mode functions
ovUnion | Pre-defined overlapping mode functions
path-method | Atena parameter class
qtex | Quantify transposable element expression
qtex-method | Quantify transposable element expression
QuantifyParam-class | Atena 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