recipe bioconductor-tilingarray

Transcript mapping with high-density oligonucleotide tiling arrays

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-tilingarray/meta.yaml

The package provides functionality that can be useful for the analysis of high-density tiling microarray data (such as from Affymetrix genechips) for measuring transcript abundance and architecture. The main functionalities of the package are: 1. the class 'segmentation' for representing partitionings of a linear series of data; 2. the function 'segment' for fitting piecewise constant models using a dynamic programming algorithm that is both fast and exact; 3. the function 'confint' for calculating confidence intervals using the strucchange package; 4. the function 'plotAlongChrom' for generating pretty plots; 5. the function 'normalizeByReference' for probe-sequence dependent response adjustment from a (set of) reference hybridizations.

package bioconductor-tilingarray

versions:

1.80.0-0,  1.78.0-0,  1.76.0-1,  1.76.0-0,  1.72.0-2,  1.72.0-1,  1.72.0-0,  1.70.0-0,  1.68.0-1, 

1.80.0-0,  1.78.0-0,  1.76.0-1,  1.76.0-0,  1.72.0-2,  1.72.0-1,  1.72.0-0,  1.70.0-0,  1.68.0-1,  1.68.0-0,  1.66.0-0,  1.64.0-0,  1.62.0-1,  1.60.0-0

depends bioconductor-affy:

>=1.80.0,<1.81.0

depends bioconductor-affy:

>=1.80.0,<1.81.0a0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-biobase:

>=2.62.0,<2.63.0a0

depends bioconductor-genefilter:

>=1.84.0,<1.85.0

depends bioconductor-genefilter:

>=1.84.0,<1.85.0a0

depends bioconductor-vsn:

>=3.70.0,<3.71.0

depends bioconductor-vsn:

>=3.70.0,<3.71.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends r-base:

>=4.3,<4.4.0a0

depends r-pixmap:

depends r-rcolorbrewer:

depends r-strucchange:

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-tilingarray

and update with::

   mamba update bioconductor-tilingarray

To create a new environment, run:

mamba create --name myenvname bioconductor-tilingarray

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-tilingarray:<tag>

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

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