atena-package: atena: analysis of transposable elements in R and...

In functionalgenomics/atena: Analysis of Transposable Elements

atena: analysis of transposable elements in R and Bioconductor

Description

The atena package provides a complete re-implementation in R of three existing methods for the quantification of transposable element (TE) expression in order to facilitate its integration into Bioconductor workflows for the analysis of RNA-seq data. The three methods are TEtranscripts (Jin et al. (2015)), ERVmap (Tokuyama et al. (2018)) and Telescope (Bendall et al.(2019)).

Details

The main functions are:

• TEtranscriptsParam - build parameter objects of the class TEtranscriptsParam-class for the TEtranscripts expression quantification method

• ERVmapParam - build parameter objects of the class ERVmapParam-class for the ERVmap expression quantification method

• TelescopeParam - build parameter objects of the class TelescopeParam-class for the Telescope expression quantification method

• qtex - call the TE expression quantification method using a previously built parameter object

For detailed information on usage, see the package vignette, by typing vignette("atena").

All questions and bug reports should be posted to the Bioconductor Support Site:

https://support.bioconductor.org

The code of the development version of the package is available at the GitHub repository:

https://github.com/functionalgenomics/atena

Author(s)

Maintainer: Beatriz Calvo-Serra [e-mail]

Authors:

• Robert Castelo [e-mail]

References

Jin Y et al. TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets. Bioinformatics. 2015;31(22):3593-3599. DOI: https://doi.org/10.1093/bioinformatics/btv422

Tokuyama M et al. ERVmap analysis reveals genome-wide transcription of human endogenous retroviruses. PNAS. 2018;115(50):12565-12572. DOI: https://doi.org/10.1073/pnas.1814589115

Bendall et al. Telescope: characterization of the retrotranscriptome by accurate estimation of transposable element expression. PLOS Comp. Biol. 2019;15(9):e1006453. DOI: https://doi.org/10.1371/journal.pcbi.1006453

See Also

Useful links:

• https://github.com/rcastelo/atena

• Report bugs at https://github.com/rcastelo/atena/issues

functionalgenomics/atena documentation built on Nov. 4, 2024, 7:33 p.m.