recipe bioconductor-tekrabber

An R package estimates the correlations of orthologs and transposable elements between two species

Homepage:

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

License:

LGPL (>=3)

Recipe:

/bioconductor-tekrabber/meta.yaml

TEKRABber is made to provide a user-friendly pipeline for comparing orthologs and transposable elements (TEs) between two species. It considers the orthology confidence between two species from BioMart to normalize expression counts and detect differentially expressed orthologs/TEs. Then it provides one to one correlation analysis for desired orthologs and TEs. There is also an app function to have a first insight on the result. Users can prepare orthologs/TEs RNA-seq expression data by their own preference to run TEKRABber following the data structure mentioned in the vignettes.

package bioconductor-tekrabber

versions:

1.6.0-0,  1.4.0-0,  1.2.0-1,  1.2.0-0

depends bioconductor-apeglm:

>=1.24.0,<1.25.0

depends bioconductor-apeglm:

>=1.24.0,<1.25.0a0

depends bioconductor-biomart:

>=2.58.0,<2.59.0

depends bioconductor-biomart:

>=2.58.0,<2.59.0a0

depends bioconductor-deseq2:

>=1.42.0,<1.43.0

depends bioconductor-deseq2:

>=1.42.0,<1.43.0a0

depends bioconductor-scbn:

>=1.20.0,<1.21.0

depends bioconductor-scbn:

>=1.20.0,<1.21.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

depends r-magrittr:

depends r-rcpp:

>=1.0.7

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-tekrabber

and update with::

   mamba update bioconductor-tekrabber

To create a new environment, run:

mamba create --name myenvname bioconductor-tekrabber

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-tekrabber:<tag>

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

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