Introduction | Getting Started | Accessing the Graphical User Interface | Local Installation | Run the Web Application with Docker (Optional) | Using DiscoRhythm from R | Background | Key Definitions for Rhythm Detection in Biological Time Series | Real-world Example Datasets | Further Background References | Available Methods | Cosinor | JTK Cycle | Lomb-Scargle | ARSER | Input Format | Example Dataset | Row Names | Column Names | Processed Metadata Table | Circular and Linear Time | DiscoRhythm Interface Walkthrough | The Interface | Select Data | Specify Dataset Parameters | Outlier Removal | Inter-sample Correlation | Principal Component Analysis | Filtering Summary | Row Selection | Period Detection | Methods | PC Fits | Using Results to Proceed | Oscillation Detection | Rhythmicity Calculation Configuration | Algorithm Restrictions | Job Submission Modes | Interactive | Report | Visualizing Results | DiscoRhythm R Usage | Data Import | discoDFtoSE | discoSEtoDF | discoCheckInput | discoDesignSummary | Outlier Detection | discoInterCorOutliers | discoPCAoutliers | discoPCA | discoRepAnalysis | Dominant Rhythmicities | discoPeriodDetection | discoODAs | Batch Execution | discoBatch | Importing Archived Sessions | Method 1 | Method 2 | Reproducing Rhythm Detection Tables | Session Info | References
Package: DiscoRhythm 1.29.0
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:
DiscoRhythm_1.29.0.tar.gz
DiscoRhythm_1.29.0.zip(r-4.7)DiscoRhythm_1.29.0.zip(r-4.6)DiscoRhythm_1.29.0.zip(r-4.5)
DiscoRhythm_1.29.0.tgz(r-4.6-any)DiscoRhythm_1.29.0.tgz(r-4.5-any)
DiscoRhythm_1.29.0.tar.gz(r-4.7-any)DiscoRhythm_1.29.0.tar.gz(r-4.6-any)
DiscoRhythm_1.29.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
DiscoRhythm/json (API)
| # 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-1.29.0(bioc 3.24)DiscoRhythm-1.28.0(bioc 3.23)
softwaretimecoursequalitycontrolvisualizationguiprincipalcomponentbioconductordata-visualizationoscillationsrhythm-detectionwebapp
Last updated from:1fc87d9baf. Checks:8 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 192 | ||
| linux-devel-x86_64 | NOTE | 326 | ||
| source / vignettes | OK | 311 | ||
| linux-release-x86_64 | NOTE | 291 | ||
| macos-release-arm64 | NOTE | 200 | ||
| macos-oldrel-arm64 | NOTE | 182 | ||
| windows-devel | NOTE | 242 | ||
| windows-release | NOTE | 234 | ||
| windows-oldrel | NOTE | 240 | ||
| wasm-release | OK | 190 |
Exports:discoAppdiscoBatchdiscoCheckInputdiscoDesignSummarydiscoDFtoSEdiscoGetODAsdiscoGetSimudiscoInterCorOutliersdiscoODAsdiscoParseMetadiscoPCAdiscoPCAoutliersdiscoPeriodDetectiondiscoRepAnalysisdiscoSEtoDF
Dependencies:abindaskpassassertthatbackportsbase64encBiobaseBiocGenericsBiocManagerBiocStylebookdownbroombslibcacachemcallrcliclustercodetoolscolorspacecolourpickercommonmarkcpp11crosstalkcurldata.tableDelayedArraydendextenddigestdplyrDTeggevaluatefarverfastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsgclusgenericsGenomicRangesggExtraggplot2gluegnmgridExtragtableheatmaplyhighrhtmltoolshtmlwidgetshttpuvhttrIRangesisobanditeratorsjquerylibjsonlitekableExtraknitrlabelinglambda.rlaterlatticelazyevallifecyclemagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmatrixTestsmemoiseMetaCyclemgcvmimeminiUInlmennetopensslotelpermutepillarpkgconfigplotlyplyrprocessxpromisespspurrrqapqvcalcR6rappdirsRColorBrewerRcppregistryrelimpreshape2rlangrmarkdownrstudioapiS4ArraysS4VectorsS7sassscalesSeqinfoseriationshinyshinyBSshinycssloadersshinydashboardshinyjssourcetoolsSparseArraystringistringrSummarizedExperimentsvglitesyssystemfontstextshapingtibbletidyrtidyselecttinytexTSPUpSetRutf8vctrsveganVennDiagramviridisviridisLitewebshotwithrxfunxml2xtableXVectoryamlzip
Readme and manuals
Help Manual
| 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 |
