Package Recipe 'bioconductor-compcoder'

recipe bioconductor-compcoder

RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/compcodeR.html
License:: GPL (>= 2)
Recipe:: /bioconductor-compcoder/meta.yaml

This package provides extensive functionality for comparing results obtained by different methods for differential expression analysis of RNAseq data. It also contains functions for simulating count data. Finally, it provides convenient interfaces to several packages for performing the differential expression analysis. These can also be used as templates for setting up and running a user-defined differential analysis workflow within the framework of the package.

package bioconductor-compcoder¶

Versions:

1.46.0-0, 1.42.0-0, 1.38.0-0, 1.36.2-0, 1.34.0-0, 1.30.0-0, 1.28.0-0, 1.26.1-0, 1.26.0-0,

1.46.0-0, 1.42.0-0, 1.38.0-0, 1.36.2-0, 1.34.0-0, 1.30.0-0, 1.28.0-0, 1.26.1-0, 1.26.0-0, 1.24.0-0, 1.22.0-0, 1.20.0-1, 1.20.0-0, 1.18.1-0, 1.18.0-0

Depends:

on bioconductor-edger >=4.8.0,<4.9.0
on bioconductor-limma >=3.66.0,<3.67.0
on r-ape
on r-base >=4.5,<4.6.0a0
on r-catools
on r-ggplot2
on r-gplots
on r-gtools
on r-kernsmooth
on r-knitr >=1.2
on r-lattice >=0.16
on r-markdown
on r-mass
on r-matrixstats
on r-modeest
on r-phylolm
on r-rmarkdown
on r-rocr
on r-shiny
on r-shinydashboard
on r-sm
on r-stringr
on r-vioplot

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-compcoder

to add into an existing workspace instead, run:

pixi add bioconductor-compcoder

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-compcoder

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-compcoder

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-compcoder:<tag>

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