- recipe bioconductor-cleanupdtseq
cleanUpdTSeq cleans up artifacts from polyadenylation sites from oligo(dT)-mediated 3' end RNA sequending data
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¶
- depends bioconductor-biostrings:
- depends bioconductor-bsgenome:
- depends bioconductor-bsgenome.drerio.ucsc.danrer7:
- depends bioconductor-genomeinfodb:
- depends bioconductor-genomicranges:
- depends bioconductor-iranges:
- depends bioconductor-s4vectors:
- depends r-base:
- depends r-e1071:
- depends r-seqinr:
- depends r-stringr:
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
myenvnamebeing 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>``)