recipe bioconductor-edaseq

Exploratory Data Analysis and Normalization for RNA-Seq

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/EDASeq.html

License:

Artistic-2.0

Recipe:

/bioconductor-edaseq/meta.yaml

Links:

biotools: edaseq

Numerical and graphical summaries of RNA-Seq read data. Within-lane normalization procedures to adjust for GC-content effect (or other gene-level effects) on read counts: loess robust local regression, global-scaling, and full-quantile normalization (Risso et al., 2011). Between-lane normalization procedures to adjust for distributional differences between lanes (e.g., sequencing depth): global-scaling and full-quantile normalization (Bullard et al., 2010).

package bioconductor-edaseq

versions:

2.36.0-0,  2.34.0-0,  2.32.0-0,  2.28.0-0,  2.26.0-0,  2.24.0-1,  2.24.0-0,  2.22.0-0,  2.20.0-0, 

2.36.0-0,  2.34.0-0,  2.32.0-0,  2.28.0-0,  2.26.0-0,  2.24.0-1,  2.24.0-0,  2.22.0-0,  2.20.0-0,  2.18.0-1,  2.16.0-0,  2.14.1-0,  2.12.0-0,  2.10.0-0,  2.8.0-0

depends bioconductor-annotationdbi:

>=1.64.0,<1.65.0

depends bioconductor-aroma.light:

>=3.32.0,<3.33.0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biomart:

>=2.58.0,<2.59.0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-genomicfeatures:

>=1.54.0,<1.55.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0

depends bioconductor-shortread:

>=1.60.0,<1.61.0

depends r-base:

>=4.3,<4.4.0a0

depends r-biocmanager:

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-edaseq

and update with::

   mamba update bioconductor-edaseq

To create a new environment, run:

mamba create --name myenvname bioconductor-edaseq

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-edaseq:<tag>

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

Download stats

Link to this page

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