recipe bioconductor-harshlight

A "corrective make-up" program for microarray chips

Homepage:

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

License:

GPL (>= 2)

Recipe:

/bioconductor-harshlight/meta.yaml

Links:

biotools: harshlight, doi: 10.1186/1471-2105-6-294

The package is used to detect extended, diffuse and compact blemishes on microarray chips. Harshlight automatically marks the areas in a collection of chips (affybatch objects) and a corrected AffyBatch object is returned, in which the defected areas are substituted with NAs or the median of the values of the same probe in the other chips in the collection. The new version handle the substitute value as whole matrix to solve the memory problem.

package bioconductor-harshlight

versions:

1.78.0-0,  1.74.0-0,  1.72.0-0,  1.70.0-1,  1.70.0-0,  1.66.0-2,  1.66.0-1,  1.66.0-0,  1.64.0-0, 

1.78.0-0,  1.74.0-0,  1.72.0-0,  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,  1.54.0-0,  1.52.0-0,  1.50.0-0

depends bioconductor-affy:

>=1.84.0,<1.85.0

depends bioconductor-affy:

>=1.84.0,<1.85.0a0

depends bioconductor-altcdfenvs:

>=2.68.0,<2.69.0

depends bioconductor-altcdfenvs:

>=2.68.0,<2.69.0a0

depends bioconductor-biobase:

>=2.66.0,<2.67.0

depends bioconductor-biobase:

>=2.66.0,<2.67.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc:

>=13

depends liblapack:

>=3.9.0,<4.0a0

depends r-base:

>=4.4,<4.5.0a0

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-harshlight

and update with::

   mamba update bioconductor-harshlight

To create a new environment, run:

mamba create --name myenvname bioconductor-harshlight

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-harshlight:<tag>

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

Download stats

Link to this page

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[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-harshlight/README.html)