Package: Trendy 1.27.0
Trendy: Breakpoint analysis of time-course expression data
Trendy implements segmented (or breakpoint) regression models to estimate breakpoints which represent changes in expression for each feature/gene in high throughput data with ordered conditions.
Authors:
Trendy_1.27.0.tar.gz
Trendy_1.27.0.zip(r-4.5)Trendy_1.27.0.zip(r-4.4)Trendy_1.27.0.zip(r-4.3)
Trendy_1.27.0.tgz(r-4.4-any)Trendy_1.27.0.tgz(r-4.3-any)
Trendy_1.27.0.tar.gz(r-4.5-noble)Trendy_1.27.0.tar.gz(r-4.4-noble)
Trendy_1.27.0.tgz(r-4.4-emscripten)Trendy_1.27.0.tgz(r-4.3-emscripten)
Trendy.pdf |Trendy.html✨
Trendy/json (API)
NEWS
# Install 'Trendy' in R: |
install.packages('Trendy', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/rhondabacher/trendy/issues
- trendyExampleData - Example dataset for Trendy
On BioConductor:Trendy-1.27.0(bioc 3.20)Trendy-1.26.0(bioc 3.19)
Last updated 2 months agofrom:2f09aad538
Exports:breakpointDistbreakpointFitextractPatternfitSegBICformatFuncformatResultsgetCountsplotFeatureresultstopTrendytrendHeatmaptrendytrendyShiny
Dependencies:abindaskpassbase64encBHBiobaseBiocGenericsBiocParallelbitopsbslibcachemcaToolsclicodetoolscommonmarkcpp11crayoncrosstalkcurlDelayedArraydigestDTevaluatefansifastmapfontawesomeformatRfsfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluegplotsgtoolshighrhtmltoolshtmlwidgetshttpuvhttrIRangesjquerylibjsonliteKernSmoothknitrlambda.rlaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimenlmeopensslpillarpkgconfigpromisesR6rappdirsRcpprlangrmarkdownS4ArraysS4VectorssasssegmentedshinyshinyFilessnowsourcetoolsSparseArraySummarizedExperimentsystibbletinytexUCSC.utilsutf8vctrswithrxfunxtableXVectoryamlzlibbioc
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Distribution of breakpoints | breakpointDist |
break point fits | breakpointFit |
Extract pattern from segmented regression | extractPattern |
Fit segmented regression models on a feature/gene | fitSegBIC |
internal helper function to format results | formatFunc |
Function to format results for saving. | formatResults |
getCounts | getCounts |
Plot features of interest | plotFeature |
results | results |
obtain top genes from trendy results | topTrendy |
Draw heatmap of gene expression trends | trendHeatmap |
Trendy | trendy |
Example dataset for Trendy | trendyExampleData |
Trendy shiny app to interactively vizualize results after running trendy(). | trendyShiny |