DiscoRhythm

DOI: 10.18129/B9.bioc.DiscoRhythm    

Interactive Workflow for Discovering Rhythmicity in Biological Data

Bioconductor version: Release (3.13)

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>

Installation

To install this package, start R (version "4.1") and enter:

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

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")

 

HTML	R Script	Introduction to DiscoRhythm
PDF		Reference Manual
Text		NEWS

Details

biocViews	GUI, PrincipalComponent, QualityControl, Software, TimeCourse, Visualization
Version	1.8.0
In Bioconductor since	BioC 3.9 (R-3.6) (2.5 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
LinkingTo
Suggests	testthat
SystemRequirements	To generate html reports pandoc (http://pandoc.org/installing.html) is required.
Enhances
URL	https://github.com/matthewcarlucci/DiscoRhythm
BugReports	https://github.com/matthewcarlucci/DiscoRhythm/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	DiscoRhythm_1.8.0.tar.gz
Windows Binary	DiscoRhythm_1.8.0.zip
macOS 10.13 (High Sierra)	DiscoRhythm_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/DiscoRhythm
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/DiscoRhythm
Package Short Url	https://bioconductor.org/packages/DiscoRhythm/
Package Downloads Report	Download Stats