recipe bioconductor-cleanuprnaseq

Detect and Correct Genomic DNA Contamination in RNA-seq Data

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/CleanUpRNAseq.html

License:

GPL-3

Recipe:

/bioconductor-cleanuprnaseq/meta.yaml

RNA-seq data generated by some library preparation methods, such as rRNA-depletion-based method and the SMART-seq method, might be contaminated by genomic DNA (gDNA), if DNase I disgestion is not performed properly during RNA preparation. CleanUpRNAseq is developed to check if RNA-seq data is suffered from gDNA contamination. If so, it can perform correction for gDNA contamination and reduce false discovery rate of differentially expressed genes.

package bioconductor-cleanuprnaseq

versions:

1.0.0-0

depends bioconductor-annotationfilter:

>=1.30.0,<1.31.0

depends bioconductor-biocgenerics:

>=0.52.0,<0.53.0

depends bioconductor-biostrings:

>=2.74.0,<2.75.0

depends bioconductor-bsgenome:

>=1.74.0,<1.75.0

depends bioconductor-deseq2:

>=1.46.0,<1.47.0

depends bioconductor-edger:

>=4.4.0,<4.5.0

depends bioconductor-ensembldb:

>=2.30.0,<2.31.0

depends bioconductor-genomeinfodb:

>=1.42.0,<1.43.0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0

depends bioconductor-limma:

>=3.62.0,<3.63.0

depends bioconductor-qsmooth:

>=1.22.0,<1.23.0

depends bioconductor-rsamtools:

>=2.22.0,<2.23.0

depends bioconductor-rsubread:

>=2.20.0,<2.21.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends bioconductor-tximport:

>=1.34.0,<1.35.0

depends r-base:

>=4.4,<4.5.0a0

depends r-ggplot2:

depends r-ggrepel:

depends r-kernsmooth:

depends r-pheatmap:

depends r-r6:

depends r-rcolorbrewer:

depends r-reshape2:

requirements:

additional platforms:

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-cleanuprnaseq

and update with::

   mamba update bioconductor-cleanuprnaseq

To create a new environment, run:

mamba create --name myenvname bioconductor-cleanuprnaseq

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-cleanuprnaseq:<tag>

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

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