recipe bioconductor-atena

Analysis of Transposable Elements

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/atena.html

License:

Artistic-2.0

Recipe:

/bioconductor-atena/meta.yaml

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.

package bioconductor-atena

Versions:

1.4.0-0,  1.0.0-0

Depends:

• bioconductor-annotationhub >=3.6.0,<3.7.0

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-biocparallel >=1.32.0,<1.33.0

• bioconductor-genomeinfodb >=1.34.0,<1.35.0

• bioconductor-genomicalignments >=1.34.0,<1.35.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-rsamtools >=2.14.0,<2.15.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-sparsematrixstats >=1.10.0,<1.11.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• r-base >=4.2,<4.3.0a0

• r-matrix

• r-matrixstats

• r-scales

• r-squarem

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-atena

and update with:

conda update bioconductor-atena

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-atena:<tag>

(see bioconductor-atena/tags for valid values for <tag>)

Download stats

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