Package Recipe 'bioconductor-ideal'

recipe bioconductor-ideal

Interactive Differential Expression AnaLysis

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/ideal.html
License:: MIT + file LICENSE
Recipe:: /bioconductor-ideal/meta.yaml

This package provides functions for an Interactive Differential Expression AnaLysis of RNA-sequencing datasets, to extract quickly and effectively information downstream the step of differential expression. A Shiny application encapsulates the whole package. Support for reproducibility of the whole analysis is provided by means of a template report which gets automatically compiled and can be stored/shared.

package bioconductor-ideal¶

Versions:

2.4.0-0, 2.0.0-0, 1.24.1-0, 1.22.0-0, 1.18.0-0, 1.16.0-0, 1.14.0-1, 1.14.0-0, 1.10.0-0,

2.4.0-0, 2.0.0-0, 1.24.1-0, 1.22.0-0, 1.18.0-0, 1.16.0-0, 1.14.0-1, 1.14.0-0, 1.10.0-0, 1.8.0-1, 1.6.0-0, 1.4.0-0, 1.2.0-0

Depends:

on bioconductor-annotationdbi >=1.72.0,<1.73.0
on bioconductor-biocparallel >=1.44.0,<1.45.0
on bioconductor-deseq2 >=1.50.0,<1.51.0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-go.db >=3.22.0,<3.23.0
on bioconductor-goseq >=1.62.0,<1.63.0
on bioconductor-gostats >=2.76.0,<2.77.0
on bioconductor-ihw >=1.38.0,<1.39.0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-limma >=3.66.0,<3.67.0
on bioconductor-mosdef >=1.6.0,<1.7.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on bioconductor-topgo >=2.62.0,<2.63.0
on r-base >=4.5,<4.6.0a0
on r-base64enc
on r-dplyr
on r-dt
on r-ggplot2 >=2.0.0
on r-ggrepel
on r-gplots
on r-heatmaply
on r-knitr
on r-pheatmap
on r-plotly
on r-rentrez
on r-rintrojs
on r-rlang
on r-rmarkdown
on r-shiny >=0.12.0
on r-shinyace
on r-shinybs
on r-shinydashboard
on r-stringr
on r-upsetr

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-ideal

to add into an existing workspace instead, run:

pixi add bioconductor-ideal

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-ideal

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-ideal

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-ideal:<tag>

(see bioconductor-ideal/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-ideal/README.html)