Package: Trendy 1.35.0

Rhonda Bacher

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:Rhonda Bacher and Ning Leng

Trendy_1.35.0.tar.gz
Trendy_1.35.0.zip(r-4.7)Trendy_1.35.0.zip(r-4.6)Trendy_1.35.0.zip(r-4.5)
Trendy_1.35.0.tgz(r-4.6-any)Trendy_1.35.0.tgz(r-4.5-any)
Trendy_1.35.0.tar.gz(r-4.7-any)Trendy_1.35.0.tar.gz(r-4.6-any)
Trendy_1.35.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Trendy/json (API)

# 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

Datasets:

trendyExampleData - Example dataset for Trendy

On BioConductor:Trendy-1.35.0(bioc 3.24)Trendy-1.34.0(bioc 3.23)

timecourse rnaseq regression immunooncology

7.18 score 7 stars 1 packages 18 scripts 8 mentions 13 exports 81 dependencies

Last updated from:2eb84050b7. Checks:1 ERROR, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	192
linux-devel-x86_64	OK	339
source / vignettes	OK	293
linux-release-x86_64	OK	346
macos-release-arm64	OK	187
macos-oldrel-arm64	OK	161
windows-devel	OK	216
windows-release	OK	168
windows-oldrel	OK	200
wasm-release	OK	176

Exports:breakpointDist breakpointFit extractPattern fitSegBIC formatFunc formatResults getCounts plotFeature results topTrendy trendHeatmap trendy trendyShiny

Dependencies:abind base64enc BH Biobase BiocGenerics BiocParallel bitops bslib cachem caTools cli codetools commonmark cpp11 crosstalk DelayedArray digest DT evaluate fastmap fontawesome formatR fs futile.logger futile.options generics GenomicRanges glue gplots gtools highr htmltools htmlwidgets httpuv IRanges jquerylib jsonlite KernSmooth knitr lambda.r later lattice lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mime nlme otel pillar pkgconfig promises R6 rappdirs Rcpp rlang rmarkdown S4Arrays S4Vectors sass segmented Seqinfo shiny shinyFiles snow sourcetools SparseArray SummarizedExperiment tibble tinytex utf8 vctrs withr xfun xtable XVector yaml

Trendy Vignette

Rendered fromTrendy_vignette.Rnwusingknitr::knitr

Last update: 2019-11-13
Started: 2018-01-08

Citation

Development and contributors

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