Package: Trendy 1.29.0

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

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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

Datasets:

trendyExampleData - Example dataset for Trendy

On BioConductor:Trendy-1.29.0(bioc 3.21)Trendy-1.28.0(bioc 3.20)

timecourse rnaseq regression immunooncology

6.49 score 6 stars 13 scripts 212 downloads 8 mentions 13 exports 90 dependencies

Last updated 23 days agofrom:e2f06d3f3e. Checks:OK: 3 WARNING: 4. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 04 2024
R-4.5-win	WARNING	Nov 04 2024
R-4.5-linux	WARNING	Nov 04 2024
R-4.4-win	WARNING	Nov 04 2024
R-4.4-mac	OK	Nov 04 2024
R-4.3-win	WARNING	Nov 04 2024
R-4.3-mac	OK	Nov 04 2024

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

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

Trendy Vignette

Rendered fromTrendy_vignette.Rnwusingknitr::knitron Nov 04 2024.

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