recipe bioconductor-oligo

Preprocessing tools for oligonucleotide arrays

Homepage:

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

License:

LGPL (>= 2)

Recipe:

/bioconductor-oligo/meta.yaml

Links:

biotools: oligo

A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).

package bioconductor-oligo

versions:

1.70.0-1,  1.70.0-0,  1.66.0-0,  1.64.1-0,  1.62.0-1,  1.62.0-0,  1.58.0-2,  1.58.0-1,  1.58.0-0, 

1.70.0-1,  1.70.0-0,  1.66.0-0,  1.64.1-0,  1.62.0-1,  1.62.0-0,  1.58.0-2,  1.58.0-1,  1.58.0-0,  1.56.0-0,  1.54.1-0,  1.54.0-0,  1.52.0-0,  1.50.0-0,  1.48.0-1,  1.46.0-0,  1.44.0-0,  1.42.0-0,  1.40.2-0,  1.40.1-0

depends bioconductor-affxparser:

>=1.78.0,<1.79.0

depends bioconductor-affxparser:

>=1.78.0,<1.79.0a0

depends bioconductor-affyio:

>=1.76.0,<1.77.0

depends bioconductor-affyio:

>=1.76.0,<1.77.0a0

depends bioconductor-biobase:

>=2.66.0,<2.67.0

depends bioconductor-biobase:

>=2.66.0,<2.67.0a0

depends bioconductor-biocgenerics:

>=0.52.0,<0.53.0

depends bioconductor-biocgenerics:

>=0.52.0,<0.53.0a0

depends bioconductor-biostrings:

>=2.74.0,<2.75.0

depends bioconductor-biostrings:

>=2.74.0,<2.75.0a0

depends bioconductor-oligoclasses:

>=1.68.0,<1.69.0

depends bioconductor-oligoclasses:

>=1.68.0,<1.69.0a0

depends bioconductor-preprocesscore:

>=1.68.0,<1.69.0

depends bioconductor-preprocesscore:

>=1.68.0,<1.69.0a0

depends bioconductor-zlibbioc:

>=1.52.0,<1.53.0

depends bioconductor-zlibbioc:

>=1.52.0,<1.53.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc:

>=13

depends liblapack:

>=3.9.0,<4.0a0

depends libzlib:

>=1.3.1,<2.0a0

depends r-base:

>=4.4,<4.5.0a0

depends r-dbi:

>=0.3.1

depends r-ff:

depends r-rsqlite:

>=1.0.0

requirements:

additional platforms:

linux-aarch64

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-oligo

and update with::

   mamba update bioconductor-oligo

To create a new environment, run:

mamba create --name myenvname bioconductor-oligo

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-oligo:<tag>

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

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