DiscoRhythm

DOI: 10.18129/B9.bioc.DiscoRhythm    

This is the development version of DiscoRhythm; to use it, please install the devel version of Bioconductor.

Interactive Workflow for Discovering Rhythmicity in Biological Data

Bioconductor version: Development (3.10)

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 "3.6") and enter:

if (!requireNamespace("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")

 

HTML R Script Introduction to DiscoRhythm
PDF   Reference Manual
Text   NEWS

Details

biocViews GUI, PrincipalComponent, QualityControl, Software, TimeCourse, Visualization
Version 1.1.1
In Bioconductor since BioC 3.9 (R-3.6) (< 6 months)
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
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_1.1.1.tar.gz
Windows Binary DiscoRhythm_1.1.1.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) DiscoRhythm_1.1.1.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

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