README.md

In Trendy: Breakpoint analysis of time-course expression data

Trendy

Trendy: Segmented regression analysis of expression dynamics for high-throughput ordered profiling experiments

Trendy utilizes segmented regression models to simultaneously characterize each gene’s expression pattern and summarize overall dynamic activity in ordered condition experiments. For each gene, Trendy finds the optimal segmented regression model and provides the location and direction of dynamic changes in expression. The top dynamic genes are then identified as genes that can be well profiled by its gene-specific segmented regression model. Trendy also implements functions to visualize the dynamic genes and their trends, to order dynamic genes by their trends, and to compute breakpoint distribution at different time points (e.g. detect time points with a large number of expression changes).

Trendy is now published in BMC Bioinformatics. If you use Trendy in your research, please cite:

Bacher R, Leng N, Chu LF, Ni Z, Thomson JA, Kendziorski C, Stewart R. Trendy: segmented regression analysis of expression dynamics in high-throughput ordered profiling experiments. BMC Bioinformatics. 2018 Dec;19(1):380.

The vignette for Trendy can be found here:

http://www.bioconductor.org/packages/release/bioc/vignettes/Trendy/inst/doc/Trendy_vignette.pdf

The current version of Trendy is now on Bioconductor: http://www.bioconductor.org/packages/release/bioc/html/Trendy.html

The vignette for Trendy can be found here:

http://www.bioconductor.org/packages/release/bioc/vignettes/Trendy/inst/doc/Trendy_vignette.pdf

For previous versions check the release page.

To install Trendy:

You need to have R version >= 3.5 installed.

Option 1:

library(BiocManager)

if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager")

BiocManager::install("Trendy")

Option 2:

install.packages("devtools")

library(devtools)

install_github("rhondabacher/Trendy")

Option 3 (For R version 3.4, note that this version is no longer being updated):

install.packages("devtools")

library(devtools)

install_github("rhondabacher/Trendy", ref="devel")

Trendy R/Shiny Visualization

Trendy R/Shiny assumes you have already run the trendy() function in the Trendy package and saved the output as an .RData object (by setting saveObject = TRUE). The app allows you to extract lists of genes/features according to any pattern of interest. The patten of interest can also be extracted after a given condition (time-point) via the Delay option. The Shiny application also enables the trend and breakpoints of each gene to be explored and visualized.

To launch the Shiny app in R:

library(Trendy)

trendyShiny()

Example of patterns:

"up,down" : Genes/Features which contain a peak through the time-course.

"down,up" : Genes/Features which contain a trough in the time-course.

Trendy documentation built on Nov. 8, 2020, 8:10 p.m.