Package Recipe 'bioconductor-rificomparative'

recipe bioconductor-rificomparative

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

Homepage:: https://bioconductor.org/packages/3.20/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:

1.10.0-0, 1.6.0-0, 1.2.0-0, 1.0.1-0

Depends:

on bioconductor-dta >=2.56.0,<2.57.0
on bioconductor-rtracklayer >=1.70.0,<1.71.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on r-base >=4.5,<4.6.0a0
on r-cowplot
on r-devtools
on r-domc
on r-dplyr
on r-egg
on r-foreach
on r-ggplot2
on r-ggrepel
on r-lsd
on r-nnet
on r-reshape2
on r-rlang
on r-scales
on r-stringr
on r-tibble
on r-writexl

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-rificomparative

to add into an existing workspace instead, run:

pixi add bioconductor-rificomparative

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-rificomparative

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-rificomparative

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-rificomparative:<tag>

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-rificomparative/README.html)