recipe bioconductor-affxparser

Affymetrix File Parsing SDK

Homepage:

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

License:

LGPL (>= 2)

Recipe:

/bioconductor-affxparser/meta.yaml

Package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). It provides methods for fast and memory efficient parsing of Affymetrix files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files are supported. Currently, there are methods for reading chip definition file (CDF) and a cell intensity file (CEL). These files can be read either in full or in part. For example, probe signals from a few probesets can be extracted very quickly from a set of CEL files into a convenient list structure.

package bioconductor-affxparser

versions:

1.78.0-0,  1.74.0-1,  1.74.0-0,  1.72.0-0,  1.70.0-2,  1.70.0-1,  1.70.0-0,  1.66.0-2,  1.66.0-1, 

1.78.0-0,  1.74.0-1,  1.74.0-0,  1.72.0-0,  1.70.0-2,  1.70.0-1,  1.70.0-0,  1.66.0-2,  1.66.0-1,  1.66.0-0,  1.64.0-0,  1.62.0-1,  1.62.0-0,  1.60.0-0,  1.58.0-0,  1.56.0-1,  1.56.0-0,  1.54.0-0,  1.52.0-0,  1.50.0-0,  1.48.0-0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc:

>=13

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx:

>=13

depends r-base:

>=4.4,<4.5.0a0

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-affxparser

and update with::

   mamba update bioconductor-affxparser

To create a new environment, run:

mamba create --name myenvname bioconductor-affxparser

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-affxparser:<tag>

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

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