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DiscoRhythm

This is the development version of DiscoRhythm; for the stable release version, see DiscoRhythm.

Interactive Workflow for Discovering Rhythmicity in Biological Data


Bioconductor version: Development (3.19)

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.

Author: Matthew Carlucci [aut, cre], Algimantas Kriščiūnas [aut], Haohan Li [aut], Povilas Gibas [aut], Karolis Koncevičius [aut], Art Petronis [aut], Gabriel Oh [aut]

Maintainer: Matthew Carlucci <Matthew.Carlucci at camh.ca>

Citation (from within R, enter citation("DiscoRhythm")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("DiscoRhythm")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("DiscoRhythm")
Introduction to DiscoRhythm HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews GUI, PrincipalComponent, QualityControl, Software, TimeCourse, Visualization
Version 1.19.0
In Bioconductor since BioC 3.9 (R-3.6) (5 years)
License GPL-3
Depends R (>= 3.6.0)
Imports matrixTests, matrixStats, MetaCycle (>= 1.2.0), data.table, ggplot2, ggExtra, dplyr, broom, shiny, shinyBS, shinycssloaders, shinydashboard, shinyjs, BiocStyle, rmarkdown, knitr, kableExtra, magick, VennDiagram, UpSetR, heatmaply, viridis, plotly, DT, gridExtra, methods, stats, SummarizedExperiment, BiocGenerics, S4Vectors, zip, reshape2
System Requirements To generate html reports pandoc (http://pandoc.org/installing.html) is required.
URL https://github.com/matthewcarlucci/DiscoRhythm
Bug Reports https://github.com/matthewcarlucci/DiscoRhythm/issues
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package DiscoRhythm_1.19.0.tar.gz
Windows Binary DiscoRhythm_1.19.0.zip
macOS Binary (x86_64) DiscoRhythm_1.19.0.tgz
macOS Binary (arm64) DiscoRhythm_1.19.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/DiscoRhythm
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DiscoRhythm
Bioc Package Browser https://code.bioconductor.org/browse/DiscoRhythm/
Package Short Url https://bioconductor.org/packages/DiscoRhythm/
Package Downloads Report Download Stats