recipe bioconductor-rificomparative

'rifiComparative' compares the output of rifi from two different conditions.

Homepage:

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

License:

GPL-3 + file LICENSE

Recipe:

/bioconductor-rificomparative/meta.yaml

'rifiComparative' is a continuation of rifi package. It compares two conditions output of rifi using half-life and mRNA at time 0 segments. As an input for the segmentation, the difference between half-life of both condtions and log2FC of the mRNA at time 0 are used. The package provides segmentation, statistics, summary table, fragments visualization and some additional useful plots for further anaylsis.

package bioconductor-rificomparative

versions:

1.2.0-0,  1.0.1-0

depends bioconductor-dta:

>=2.48.0,<2.49.0

depends bioconductor-rtracklayer:

>=1.62.0,<1.63.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-cowplot:

depends r-devtools:

depends r-domc:

depends r-dplyr:

depends r-egg:

depends r-foreach:

depends r-ggplot2:

depends r-ggrepel:

depends r-lsd:

depends r-nnet:

depends r-reshape2:

depends r-rlang:

depends r-scales:

depends r-stringr:

depends r-tibble:

depends r-writexl:

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-rificomparative

and update with::

   mamba update bioconductor-rificomparative

To create a new environment, run:

mamba create --name myenvname bioconductor-rificomparative

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-rificomparative:<tag>

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

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Link to this page

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