Package: DiscoRhythm 1.21.0

Matthew Carlucci

DiscoRhythm: Interactive Workflow for Discovering Rhythmicity in Biological Data

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.

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

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DiscoRhythm.pdf |DiscoRhythm.html✨
DiscoRhythm/json (API)
NEWS

# Install 'DiscoRhythm' in R:

install.packages('DiscoRhythm', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/matthewcarlucci/discorhythm/issues

Datasets:

discoODAexclusionMatrix - Algorithm Exclusion Matrix
discoODAid2name - Mapping Identifiers to Full Names

On BioConductor:DiscoRhythm-1.21.0(bioc 3.20)DiscoRhythm-1.20.0(bioc 3.19)

bioconductor-package

15 exports 0.71 score 149 dependencies 2 mentions

Last updated 2 months agofrom:6ee1cd1346

Exports:discoApp discoBatch discoCheckInput discoDesignSummary discoDFtoSE discoGetODAs discoGetSimu discoInterCorOutliers discoODAs discoParseMeta discoPCA discoPCAoutliers discoPeriodDetection discoRepAnalysis discoSEtoDF

Dependencies:abind askpass assertthat backports base64enc Biobase BiocGenerics BiocManager BiocStyle bookdown broom bslib ca cachem callr cli cluster codetools colorspace colourpicker commonmark cpp11 crayon crosstalk curl data.table DelayedArray dendextend digest dplyr DT egg evaluate fansi farver fastmap fontawesome foreach formatR fs futile.logger futile.options gclus generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggExtra ggplot2 glue gnm gridExtra gtable heatmaply highr htmltools htmlwidgets httpuv httr IRanges isoband iterators jquerylib jsonlite kableExtra knitr labeling lambda.r later lattice lazyeval lifecycle magick magrittr MASS Matrix MatrixGenerics matrixStats matrixTests memoise MetaCycle mgcv mime miniUI munsell nlme nnet openssl permute pillar pkgconfig plotly plyr processx promises ps purrr qap qvcalc R6 rappdirs RColorBrewer Rcpp registry relimp reshape2 rlang rmarkdown rstudioapi S4Arrays S4Vectors sass scales seriation shiny shinyBS shinycssloaders shinydashboard shinyjs sourcetools SparseArray stringi stringr SummarizedExperiment svglite sys systemfonts tibble tidyr tidyselect tinytex TSP UCSC.utils UpSetR utf8 vctrs vegan VennDiagram viridis viridisLite webshot withr xfun xml2 xtable XVector yaml zip zlibbioc

Introduction to r BiocStyle::Biocpkg('DiscoRhythm')

Matthew Carlucci, Algimantas Kriščiūnas, Haohan Li, Povilas Gibas, Karolis Koncevičius, Art Petronis, Gabriel Oh

Rendered fromdisco_workflow_vignette.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2020-09-29
Started: 2019-04-05

Help page	Topics
Launch the DiscoRhythm Shiny Application	discoApp
Core DiscoRhythm Workflow	discoBatch
Import Data for DiscoRhythm Analysis	discoCheckInput
Summarize the experimental design	discoDesignSummary
Data formatting for DiscoRhythm	discoDFtoSE discoSEtoDF
Read in the DiscoRhythm Simulated dataset	discoGetSimu
Algorithm Exclusion Matrix	discoODAexclusionMatrix
Mapping Identifiers to Full Names	discoODAid2name
Execute Oscillation Detection Using DiscoRhythm	discoGetODAs discoODAs
Generate Experiment Metadata	discoParseMeta
Perform PCA	discoPCA
Detect dataset-wide fits to multiple periodicities	discoPeriodDetection
Quality Control for DiscoRhythm	discoInterCorOutliers discoPCAoutliers discoQC discoRepAnalysis

Package: DiscoRhythm 1.21.0

DiscoRhythm: Interactive Workflow for Discovering Rhythmicity in Biological Data

Introduction to r BiocStyle::Biocpkg('DiscoRhythm')

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)