Package Recipe 'bioconductor-cleanuprnaseq'

recipe bioconductor-cleanuprnaseq

Detect and Correct Genomic DNA Contamination in RNA-seq Data

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/CleanUpRNAseq.html
License:: GPL-3
Recipe:: /bioconductor-cleanuprnaseq/meta.yaml

RNA-seq data generated by some library preparation methods, such as rRNA-depletion-based method and the SMART-seq method, might be contaminated by genomic DNA (gDNA), if DNase I disgestion is not performed properly during RNA preparation. CleanUpRNAseq is developed to check if RNA-seq data is suffered from gDNA contamination. If so, it can perform correction for gDNA contamination and reduce false discovery rate of differentially expressed genes.

package bioconductor-cleanuprnaseq¶

Versions:

1.4.0-0, 1.0.0-0

Depends:

on bioconductor-annotationfilter >=1.34.0,<1.35.0
on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-biostrings >=2.78.0,<2.79.0
on bioconductor-bsgenome >=1.78.0,<1.79.0
on bioconductor-deseq2 >=1.50.0,<1.51.0
on bioconductor-edger >=4.8.0,<4.9.0
on bioconductor-ensembldb >=2.34.0,<2.35.0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-limma >=3.66.0,<3.67.0
on bioconductor-qsmooth >=1.26.0,<1.27.0
on bioconductor-rsamtools >=2.26.0,<2.27.0
on bioconductor-rsubread >=2.24.0,<2.25.0
on bioconductor-seqinfo >=1.0.0,<1.1.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on bioconductor-tximport >=1.38.0,<1.39.0
on r-base >=4.5,<4.6.0a0
on r-ggplot2
on r-ggrepel
on r-kernsmooth
on r-pheatmap
on r-r6
on r-rcolorbrewer
on r-reshape2

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-cleanuprnaseq

to add into an existing workspace instead, run:

pixi add bioconductor-cleanuprnaseq

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-cleanuprnaseq

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-cleanuprnaseq

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-cleanuprnaseq:<tag>

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