recipe r-isogene

Offers framework for testing for monotonic relationship between gene expression and doses in a microarray experiment. Several testing procedures including the global likelihood-ratio test (Bartholomew, 1961), Williams (1971, 1972), Marcus (1976), M (Hu et al. 2005) and the modified M (Lin et al. 2007) are used to test for the monotonic trend in gene expression with respect to doses. BH (Benjamini and Hochberg 1995) and BY (Benjamini and Yekutieli 2004) FDR controlling procedures are applied to adjust the raw p-values obtained from the permutations.

Homepage:

https://CRAN.R-project.org/package=IsoGene

License:

GPL3 / GPL-3

Recipe:

/r-isogene/meta.yaml

package r-isogene

(downloads) docker_r-isogene

versions:

1.0_24-7,  1.0_24-6,  1.0_24-5,  1.0_24-4,  1.0_24-3,  1.0_24-2,  1.0_24-1,  1.0_24-0

depends bioconductor-affy:

depends bioconductor-biobase:

depends r-base:

>=4.3,<4.4.0a0

depends r-ff:

>=2.0.0

depends r-iso:

depends r-xtable:

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 r-isogene

and update with::

   mamba update r-isogene

To create a new environment, run:

mamba create --name myenvname r-isogene

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/r-isogene:<tag>

(see `r-isogene/tags`_ for valid values for ``<tag>``)

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Link to this page

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