DiscoRhythm
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see DiscoRhythm.
Interactive Workflow for Discovering Rhythmicity in Biological Data
Bioconductor version: 3.9
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("DiscoRhythm")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("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")| Introduction to DiscoRhythm | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GUI, PrincipalComponent, QualityControl, Software, TimeCourse, Visualization |
| Version | 1.0.0 |
| 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 |
| 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 |
See More
| Suggests | testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | DiscoRhythm_1.0.0.tar.gz |
| Windows Binary | DiscoRhythm_1.0.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | DiscoRhythm_1.0.0.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 |
| Old Source Packages for BioC 3.9 | Source Archive |