Package: DiscoRhythm 1.23.0
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_1.23.0.tar.gz
DiscoRhythm_1.23.0.zip(r-4.5)DiscoRhythm_1.23.0.zip(r-4.4)DiscoRhythm_1.23.0.zip(r-4.3)
DiscoRhythm_1.23.0.tgz(r-4.5-any)DiscoRhythm_1.23.0.tgz(r-4.4-any)DiscoRhythm_1.23.0.tgz(r-4.3-any)
DiscoRhythm_1.23.0.tar.gz(r-4.5-noble)DiscoRhythm_1.23.0.tar.gz(r-4.4-noble)
DiscoRhythm_1.23.0.tgz(r-4.4-emscripten)DiscoRhythm_1.23.0.tgz(r-4.3-emscripten)
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
- discoODAexclusionMatrix - Algorithm Exclusion Matrix
- discoODAid2name - Mapping Identifiers to Full Names
On BioConductor:DiscoRhythm-1.23.0(bioc 3.21)DiscoRhythm-1.22.0(bioc 3.20)
softwaretimecoursequalitycontrolvisualizationguiprincipalcomponentbioconductordata-visualizationoscillationsrhythm-detectionwebapp
Last updated 4 months agofrom:9e4ec1f7b1. Checks:1 OK, 6 NOTE, 1 WARNING. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Jan 28 2025 |
| R-4.5-win | NOTE | Jan 28 2025 |
| R-4.5-mac | WARNING | Jan 28 2025 |
| R-4.5-linux | NOTE | Jan 28 2025 |
| R-4.4-win | NOTE | Jan 28 2025 |
| R-4.4-mac | NOTE | Jan 28 2025 |
| R-4.3-win | NOTE | Jan 28 2025 |
| R-4.3-mac | NOTE | Jan 28 2025 |
Exports:discoAppdiscoBatchdiscoCheckInputdiscoDesignSummarydiscoDFtoSEdiscoGetODAsdiscoGetSimudiscoInterCorOutliersdiscoODAsdiscoParseMetadiscoPCAdiscoPCAoutliersdiscoPeriodDetectiondiscoRepAnalysisdiscoSEtoDF
Dependencies:abindaskpassassertthatbackportsbase64encBiobaseBiocGenericsBiocManagerBiocStylebookdownbroombslibcacachemcallrcliclustercodetoolscolorspacecolourpickercommonmarkcpp11crayoncrosstalkcurldata.tableDelayedArraydendextenddigestdplyrDTeggevaluatefansifarverfastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsgclusgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggExtraggplot2gluegnmgridExtragtableheatmaplyhighrhtmltoolshtmlwidgetshttpuvhttrIRangesisobanditeratorsjquerylibjsonlitekableExtraknitrlabelinglambda.rlaterlatticelazyevallifecyclemagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmatrixTestsmemoiseMetaCyclemgcvmimeminiUImunsellnlmennetopensslpermutepillarpkgconfigplotlyplyrprocessxpromisespspurrrqapqvcalcR6rappdirsRColorBrewerRcppregistryrelimpreshape2rlangrmarkdownrstudioapiS4ArraysS4VectorssassscalesseriationshinyshinyBSshinycssloadersshinydashboardshinyjssourcetoolsSparseArraystringistringrSummarizedExperimentsvglitesyssystemfontstibbletidyrtidyselecttinytexTSPUCSC.utilsUpSetRutf8vctrsveganVennDiagramviridisviridisLitewebshotwithrxfunxml2xtableXVectoryamlzip
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 |
