recipe bioconductor-tadar

Transcriptome Analysis of Differential Allelic Representation

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-tadar/meta.yaml

This package provides functions to standardise the analysis of Differential Allelic Representation (DAR). DAR compromises the integrity of Differential Expression analysis results as it can bias expression, influencing the classification of genes (or transcripts) as being differentially expressed. DAR analysis results in an easy-to-interpret value between 0 and 1 for each genetic feature of interest, where 0 represents identical allelic representation and 1 represents complete diversity. This metric can be used to identify features prone to false-positive calls in Differential Expression analysis, and can be leveraged with statistical methods to alleviate the impact of such artefacts on RNA-seq data.

package bioconductor-tadar

versions:

1.0.0-0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-gviz:

>=1.46.0,<1.47.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-matrixgenerics:

>=1.14.0,<1.15.0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-variantannotation:

>=1.48.0,<1.49.0

depends r-base:

>=4.3,<4.4.0a0

depends r-ggplot2:

depends r-rlang:

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-tadar

and update with::

   mamba update bioconductor-tadar

To create a new environment, run:

mamba create --name myenvname bioconductor-tadar

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-tadar:<tag>

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

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Link to this page

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