recipe bioconductor-cleanupdtseq

cleanUpdTSeq cleans up artifacts from polyadenylation sites from oligo(dT)-mediated 3' end RNA sequending data

Homepage

https://bioconductor.org/packages/3.13/bioc/html/cleanUpdTSeq.html

License

GPL-2

Recipe

/bioconductor-cleanupdtseq/meta.yaml

Links

biotools: cleanupdtseq

This package implements a Naive Bayes classifier for accurately differentiating true polyadenylation sites (pA sites) from oligo(dT)-mediated 3' end sequencing such as PAS-Seq, PolyA-Seq and RNA-Seq by filtering out false polyadenylation sites, mainly due to oligo(dT)-mediated internal priming during reverse transcription. The classifer is highly accurate and outperforms other heuristic methods.

package bioconductor-cleanupdtseq

Versions

1.30.0-0,  1.28.0-1,  1.28.0-0,  1.26.0-0,  1.24.0-0,  1.22.2-0,  1.20.0-0,  1.18.0-0,  1.16.0-0

Depends

• bioconductor-biostrings >=2.60.0,<2.61.0

• bioconductor-bsgenome >=1.60.0,<1.61.0

• bioconductor-bsgenome.drerio.ucsc.danrer7 >=1.4.0,<1.5.0

• bioconductor-genomeinfodb >=1.28.0,<1.29.0

• bioconductor-genomicranges >=1.44.0,<1.45.0

• bioconductor-iranges >=2.26.0,<2.27.0

• r-base >=4.1,<4.2.0a0

• r-e1071

• r-seqinr

• r-stringr

Required By

• bioconductor-inpas

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-cleanupdtseq

and update with:

conda update bioconductor-cleanupdtseq

or use the docker container:

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

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

Link to this page

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