recipe bioconductor-protgear

Protein Micro Array Data Management and Interactive Visualization

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/protGear.html

License:

GPL-3

Recipe:

/bioconductor-protgear/meta.yaml

A generic three-step pre-processing package for protein microarray data. This package contains different data pre-processing procedures to allow comparison of their performance.These steps are background correction, the coefficient of variation (CV) based filtering, batch correction and normalization.

package bioconductor-protgear

(downloads) docker_bioconductor-protgear

versions:

1.6.0-01.4.0-01.2.0-0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-genefilter:

>=1.84.0,<1.85.0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends bioconductor-vsn:

>=3.70.0,<3.71.0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

>=1.14.0

depends r-dplyr:

>=0.8.0

depends r-factoextra:

>=1.0.7

depends r-factominer:

>=2.4

depends r-flexdashboard:

>=0.5.2

depends r-ggally:

>=2.1.2

depends r-ggplot2:

>=3.3.0

depends r-ggpubr:

>=0.4.0

depends r-gtools:

>=3.8.2

depends r-htmltools:

>=0.4.0

depends r-kendall:

>=2.2

depends r-knitr:

>=1.33

depends r-magrittr:

>=1.5

depends r-mass:

>=7.3

depends r-pheatmap:

>=1.0.12

depends r-plotly:

>=4.9.0

depends r-plyr:

>=1.8.6

depends r-purrr:

>=0.3.4

depends r-readr:

>=2.0.1

depends r-remotes:

>=2.4.0

depends r-rlang:

>=0.4.11

depends r-rmarkdown:

>=2.9

depends r-shiny:

>=1.0.0

depends r-shinydashboard:

>=0.7.1

depends r-styler:

>=1.6.1

depends r-tibble:

>=3.1.0

depends r-tidyr:

>=1.1.3

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-protgear

and update with::

   mamba update bioconductor-protgear

To create a new environment, run:

mamba create --name myenvname bioconductor-protgear

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/bioconductor-protgear:<tag>

(see `bioconductor-protgear/tags`_ for valid values for ``<tag>``)

Download stats