Package: atena 1.19.1

Robert Castelo

atena: Analysis of Transposable Elements

Quantify expression of transposable elements (TEs) from RNA-seq data through different methods, including ERVmap, TEtranscripts and Telescope. A common interface is provided to use each of these methods, which consists of building a parameter object, calling the quantification function with this object and getting a SummarizedExperiment object as output container of the quantified expression profiles. The implementation allows one to quantify TEs and gene transcripts in an integrated manner.

Authors:Beatriz Calvo-Serra [aut], Robert Castelo [aut, cre]

atena_1.19.1.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
atena/json (API)

# Install 'atena' in R:

install.packages('atena', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rcastelo/atena/issues

On BioConductor:atena-1.19.0(bioc 3.24)atena-1.18.0(bioc 3.23)

transcription transcriptomics rnaseq sequencing preprocessing software geneexpression coverage differentialexpression functionalgenomics

6.24 score 14 stars 4 scripts 461 downloads 19 exports 91 dependencies

Last updated from:afce0c7b8e. Checks:1 WARNING, 7 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	257
linux-devel-x86_64	ERROR	306
source / vignettes	OK	805
linux-release-x86_64	ERROR	332
macos-release-arm64	ERROR	178
macos-oldrel-arm64	ERROR	137
windows-devel	ERROR	138
windows-release	ERROR	174
windows-oldrel	ERROR	148
wasm-release	OK	196

Exports:annotaTEs atenaParam ERVmapParam features getDNAtransposons getLINEs getLTRs getSINEs OneCodeToFindThemAll ovIntersectionStrict ovUnion path qtex rmskatenaparser rmskbasicparser rmskidentity show TelescopeParam TEtranscriptsParam

Dependencies:abind AnnotationDbi AnnotationHub askpass BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel BiocVersion Biostrings bit bit64 bitops blob cachem cigarillo cli codetools cpp11 crayon curl DBI dbplyr DelayedArray dplyr fastmap filelock formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges glue httr httr2 IRanges jsonlite KEGGREST lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig png purrr R6 rappdirs Rcpp RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors Seqinfo snow SparseArray sparseMatrixStats SQUAREM stringi stringr SummarizedExperiment sys tibble tidyr tidyselect UCSC.utils utf8 vctrs withr XML XVector yaml

An introduction to the atena package

Rendered fromatena.Rmdusingknitr::rmarkdown

Last update: 2024-04-24
Started: 2021-02-02

Citation

Development and contributors

Readme and manuals

Help Manual

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