atena
Analysis of Transposable Elements
Bioconductor version: Release (3.20)
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.
Author: Beatriz Calvo-Serra [aut], Robert Castelo [aut, cre]
Maintainer: Robert Castelo <robert.castelo at upf.edu>
citation("atena")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("atena")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("atena")| An introduction to the atena package | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Coverage, DifferentialExpression, FunctionalGenomics, GeneExpression, Preprocessing, RNASeq, Sequencing, Software, Transcription, Transcriptomics |
| Version | 1.12.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (3 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.3.0), SummarizedExperiment |
| Imports | methods, stats, Matrix, BiocGenerics, MatrixGenerics, BiocParallel, S4Vectors, IRanges, GenomicFeatures, GenomicRanges, GenomicAlignments, Rsamtools, GenomeInfoDb, SQUAREM, sparseMatrixStats, AnnotationHub, matrixStats, cli |
| System Requirements | |
| URL | https://github.com/rcastelo/atena |
| Bug Reports | https://github.com/rcastelo/atena/issues |
See More
| Suggests | covr, BiocStyle, knitr, rmarkdown, RUnit, TxDb.Dmelanogaster.UCSC.dm6.ensGene, RColorBrewer |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | atena_1.12.0.tar.gz |
| Windows Binary (x86_64) | atena_1.12.0.zip |
| macOS Binary (x86_64) | atena_1.12.0.tgz |
| macOS Binary (arm64) | atena_1.12.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/atena |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/atena |
| Bioc Package Browser | https://code.bioconductor.org/browse/atena/ |
| Package Short Url | https://bioconductor.org/packages/atena/ |
| Package Downloads Report | Download Stats |