Package Recipe 'bioconductor-rmmquant'

recipe bioconductor-rmmquant

RNA-Seq multi-mapping Reads Quantification Tool

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

RNA-Seq is currently used routinely, and it provides accurate information on gene transcription. However, the method cannot accurately estimate duplicated genes expression. Several strategies have been previously used, but all of them provide biased results. With Rmmquant, if a read maps at different positions, the tool detects that the corresponding genes are duplicated; it merges the genes and creates a merged gene. The counts of ambiguous reads is then based on the input genes and the merged genes. Rmmquant is a drop-in replacement of the widely used tools findOverlaps and featureCounts that handles multi-mapping reads in an unabiased way.

package bioconductor-rmmquant¶

Versions:

1.28.0-0, 1.24.0-0, 1.20.0-0, 1.18.0-0, 1.16.0-1, 1.16.0-0, 1.12.0-2, 1.12.0-1, 1.12.0-0,

1.28.0-0, 1.24.0-0, 1.20.0-0, 1.18.0-0, 1.16.0-1, 1.16.0-0, 1.12.0-2, 1.12.0-1, 1.12.0-0, 1.10.0-0, 1.8.1-0, 1.8.0-0, 1.6.0-0, 1.4.0-1, 1.2.0-1, 1.0.0-0

Depends:

on bioconductor-apeglm >=1.32.0,<1.33.0
on bioconductor-apeglm >=1.32.0,<1.33.0a0
on bioconductor-biocstyle >=2.38.0,<2.39.0
on bioconductor-biocstyle >=2.38.0,<2.39.0a0
on bioconductor-deseq2 >=1.50.0,<1.51.0
on bioconductor-deseq2 >=1.50.2,<1.51.0a0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-genomicranges >=1.62.1,<1.63.0a0
on bioconductor-org.mm.eg.db >=3.22.0,<3.23.0
on bioconductor-org.mm.eg.db >=3.22.0,<3.23.0a0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-s4vectors >=0.48.0,<0.49.0a0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0a0
on bioconductor-tbx20bamsubset >=1.46.0,<1.47.0
on bioconductor-tbx20bamsubset >=1.46.0,<1.47.0a0
on bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0
on bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.2,<3.3.0a0
on libblas >=3.9.0,<4.0a0
on libgcc >=14
on liblapack >=3.9.0,<4.0a0
on liblzma >=5.8.2,<6.0a0
on libstdcxx >=14
on libzlib >=1.3.1,<2.0a0
on r-base >=4.5,<4.6.0a0
on r-devtools
on r-rcpp >=0.12.8

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-rmmquant

to add into an existing workspace instead, run:

pixi add bioconductor-rmmquant

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-rmmquant

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-rmmquant

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-rmmquant:<tag>

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