Package Recipe 'bioconductor-discorhythm'

recipe bioconductor-discorhythm

Interactive Workflow for Discovering Rhythmicity in Biological Data

Homepage:: https://bioconductor.org/packages/3.20/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:

1.26.0-0, 1.22.0-0, 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,

1.26.0-0, 1.22.0-0, 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:

on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-biocstyle >=2.38.0,<2.39.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on pandoc
on r-base >=4.5,<4.6.0a0
on r-broom
on r-data.table
on r-dplyr
on r-dt
on r-ggextra
on r-ggplot2
on r-gridextra
on r-heatmaply
on r-kableextra
on r-knitr
on r-magick
on r-matrixstats
on r-matrixtests
on r-metacycle >=1.2.0
on r-plotly
on r-reshape2
on r-rmarkdown
on r-shiny
on r-shinybs
on r-shinycssloaders
on r-shinydashboard
on r-shinyjs
on r-upsetr
on r-venndiagram
on r-viridis
on r-zip

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-discorhythm

to add into an existing workspace instead, run:

pixi add bioconductor-discorhythm

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-discorhythm

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-discorhythm

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-discorhythm:<tag>

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