recipe bioconductor-cleanupdtseq

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

Homepage:

https://bioconductor.org/packages/3.17/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:

1.38.0-0,  1.36.0-0,  1.32.0-0,  1.30.0-0,  1.28.0-1,  1.28.0-0,  1.26.0-0,  1.24.0-0,  1.22.2-0, 

1.38.0-0,  1.36.0-0,  1.32.0-0,  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:

>=2.68.0,<2.69.0

depends bioconductor-bsgenome:

>=1.68.0,<1.69.0

depends bioconductor-bsgenome.drerio.ucsc.danrer7:

>=1.4.0,<1.5.0

depends bioconductor-genomeinfodb:

>=1.36.0,<1.37.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-iranges:

>=2.34.0,<2.35.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends r-base:

>=4.3,<4.4.0a0

depends r-e1071:

depends r-seqinr:

depends r-stringr:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-cleanupdtseq

and update with::

   mamba update bioconductor-cleanupdtseq

To create a new environment, run:

mamba create --name myenvname bioconductor-cleanupdtseq

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

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

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