recipe bioconductor-ngsreports

Load FastqQC reports and other NGS related files

Homepage:

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

License:

file LICENSE

Recipe:

/bioconductor-ngsreports/meta.yaml

This package provides methods and object classes for parsing FastQC reports and output summaries from other NGS tools into R. As well as parsing files, multiple plotting methods have been implemented for visualising the parsed data. Plots can be generated as static ggplot objects or interactive plotly objects.

package bioconductor-ngsreports

versions:

2.4.0-0,  2.2.4-0,  2.0.0-0,  1.10.0-0,  1.8.0-0,  1.6.1-0,  1.6.0-0,  1.4.0-0,  1.2.0-0, 

2.4.0-0,  2.2.4-0,  2.0.0-0,  1.10.0-0,  1.8.0-0,  1.6.1-0,  1.6.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-1

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends r-base:

>=4.3,<4.4.0a0

depends r-checkmate:

depends r-dplyr:

>=1.1.0

depends r-dt:

depends r-forcats:

depends r-ggdendro:

depends r-ggplot2:

>=3.4.0

depends r-jsonlite:

depends r-lifecycle:

depends r-lubridate:

depends r-pander:

depends r-patchwork:

>=1.1.1

depends r-plotly:

>=4.9.4

depends r-readr:

depends r-reshape2:

depends r-rlang:

depends r-rmarkdown:

depends r-scales:

depends r-stringr:

depends r-tibble:

>=1.3.1

depends r-tidyr:

depends r-tidyselect:

>=0.2.3

depends r-zoo:

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-ngsreports

and update with::

   mamba update bioconductor-ngsreports

To create a new environment, run:

mamba create --name myenvname bioconductor-ngsreports

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-ngsreports:<tag>

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

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