recipe bioconductor-discorhythm

Interactive Workflow for Discovering Rhythmicity in Biological Data

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-discorhythm/meta.yaml

Set of functions for estimation of cyclical characteristics, such as period, phase, amplitude, and statistical significance in large temporal datasets. Supporting functions are available for quality control, dimensionality reduction, spectral analysis, and analysis of experimental replicates. Contains a R Shiny web interface to execute all workflow steps.

package bioconductor-discorhythm

versions:

1.18.0-0,  1.16.0-0,  1.14.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-1,  1.6.0-0,  1.4.0-0,  1.0.0-1

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biocstyle:

>=2.30.0,<2.31.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends pandoc:

depends r-base:

>=4.3,<4.4.0a0

depends r-broom:

depends r-data.table:

depends r-dplyr:

depends r-dt:

depends r-ggextra:

depends r-ggplot2:

depends r-gridextra:

depends r-heatmaply:

depends r-kableextra:

depends r-knitr:

depends r-magick:

depends r-matrixstats:

depends r-matrixtests:

depends r-metacycle:

>=1.2.0

depends r-plotly:

depends r-reshape2:

depends r-rmarkdown:

depends r-shiny:

depends r-shinybs:

depends r-shinycssloaders:

depends r-shinydashboard:

depends r-shinyjs:

depends r-upsetr:

depends r-venndiagram:

depends r-viridis:

depends r-zip:

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-discorhythm

and update with::

   mamba update bioconductor-discorhythm

To create a new environment, run:

mamba create --name myenvname bioconductor-discorhythm

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-discorhythm:<tag>

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

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