recipe bioconductor-harshlight

A "corrective make-up" program for microarray chips

Homepage

https://bioconductor.org/packages/3.11/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

1.60.0-0,  1.58.0-0,  1.56.0-1,  1.54.0-0,  1.52.0-0,  1.50.0-0

Depends

• bioconductor-affy >=1.66.0,<1.67.0

• bioconductor-altcdfenvs >=2.50.0,<2.51.0

• bioconductor-biobase >=2.48.0,<2.49.0

• libblas >=3.8.0,<4.0a0

• libgcc-ng >=7.3.0

• liblapack >=3.8.0,<3.9.0a0

• r-base >=4.0,<4.1.0a0

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-harshlight

and update with:

conda update bioconductor-harshlight

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-harshlight:<tag>

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

Link to this page

Render an badge with the following MarkDown:

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