Package Recipe 'bioconductor-metaseqr2'

recipe bioconductor-metaseqr2

An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/metaseqR2.html
License:: GPL (>= 3)
Recipe:: /bioconductor-metaseqr2/meta.yaml

Provides an interface to several normalization and statistical testing packages for RNA-Seq gene expression data. Additionally, it creates several diagnostic plots, performs meta-analysis by combinining the results of several statistical tests and reports the results in an interactive way.

package bioconductor-metaseqr2¶

Versions:

1.22.0-0, 1.18.0-0, 1.10.0-1, 1.10.0-0, 1.6.1-1, 1.6.1-0, 1.6.0-0, 1.4.0-1, 1.4.0-0,

1.22.0-0, 1.18.0-0, 1.10.0-1, 1.10.0-0, 1.6.1-1, 1.6.1-0, 1.6.0-0, 1.4.0-1, 1.4.0-0, 1.2.0-1, 1.2.0-0, 1.0.11-0

Depends:

on bioconductor-absseq >=1.64.0,<1.65.0
on bioconductor-absseq >=1.64.0,<1.65.0a0
on bioconductor-biobase >=2.70.0,<2.71.0
on bioconductor-biobase >=2.70.0,<2.71.0a0
on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-biocgenerics >=0.56.0,<0.57.0a0
on bioconductor-biocparallel >=1.44.0,<1.45.0
on bioconductor-biocparallel >=1.44.0,<1.45.0a0
on bioconductor-biomart >=2.66.0,<2.67.0
on bioconductor-biomart >=2.66.0,<2.67.0a0
on bioconductor-biostrings >=2.78.0,<2.79.0
on bioconductor-biostrings >=2.78.0,<2.79.0a0
on bioconductor-deseq2 >=1.50.0,<1.51.0
on bioconductor-deseq2 >=1.50.2,<1.51.0a0
on bioconductor-dss >=2.58.0,<2.59.0
on bioconductor-dss >=2.58.0,<2.59.0a0
on bioconductor-edaseq >=2.44.0,<2.45.0
on bioconductor-edaseq >=2.44.0,<2.45.0a0
on bioconductor-edger >=4.8.0,<4.9.0
on bioconductor-edger >=4.8.2,<4.9.0a0
on bioconductor-genefilter >=1.92.0,<1.93.0
on bioconductor-genefilter >=1.92.0,<1.93.0a0
on bioconductor-genomeinfodb >=1.46.0,<1.47.0
on bioconductor-genomeinfodb >=1.46.2,<1.47.0a0
on bioconductor-genomicalignments >=1.46.0,<1.47.0
on bioconductor-genomicalignments >=1.46.0,<1.47.0a0
on bioconductor-genomicfeatures >=1.62.0,<1.63.0
on bioconductor-genomicfeatures >=1.62.0,<1.63.0a0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-genomicranges >=1.62.1,<1.63.0a0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-iranges >=2.44.0,<2.45.0a0
on bioconductor-limma >=3.66.0,<3.67.0
on bioconductor-limma >=3.66.0,<3.67.0a0
on bioconductor-qvalue >=2.42.0,<2.43.0
on bioconductor-qvalue >=2.42.0,<2.43.0a0
on bioconductor-rsamtools >=2.26.0,<2.27.0
on bioconductor-rsamtools >=2.26.0,<2.27.0a0
on bioconductor-rtracklayer >=1.70.0,<1.71.0
on bioconductor-rtracklayer >=1.70.1,<1.71.0a0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-s4vectors >=0.48.0,<0.49.0a0
on bioconductor-seqinfo >=1.0.0,<1.1.0
on bioconductor-seqinfo >=1.0.0,<1.1.0a0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0a0
on bioconductor-survcomp >=1.60.0,<1.61.0
on bioconductor-survcomp >=1.60.0,<1.61.0a0
on bioconductor-txdbmaker >=1.6.0,<1.7.0
on bioconductor-txdbmaker >=1.6.2,<1.7.0a0
on bioconductor-vsn >=3.78.0,<3.79.0
on bioconductor-vsn >=3.78.1,<3.79.0a0
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 libzlib >=1.3.1,<2.0a0
on r-base >=4.5,<4.6.0a0
on r-corrplot
on r-dt
on r-gplots
on r-harmonicmeanp
on r-heatmaply
on r-htmltools
on r-httr
on r-jsonlite
on r-lattice
on r-locfit
on r-log4r
on r-magrittr
on r-mass
on r-matrix
on r-nbpseq
on r-pander
on r-rmarkdown
on r-rmdformats
on r-rsqlite
on r-stringr
on r-venndiagram
on r-yaml
on r-zoo

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-metaseqr2

to add into an existing workspace instead, run:

pixi add bioconductor-metaseqr2

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-metaseqr2

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-metaseqr2

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-metaseqr2:<tag>

(see bioconductor-metaseqr2/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-metaseqr2/README.html)