IsoformVisRNA is an R Package that generates plots to compare
transcript-level expression counts. It takes normalized count matrices
generated by kallisto and its corresponding metadata for its analysis.
This package have functions to generate figures like box plots and bar
plots to compare the expression ratios of various transcripts in a gene.
This package will improve the workflow in the analysis a gene’s
alternative splicing and help determine the dominant splicing pattern in
samples. The IsoformVisRNA package was developed using
R version 4.3.1 (2023-06-16),
Platform: x86_64-apple-darwin20 (64-bit) and
Running under: macOS Monterey 12.3.1.
To install the latest version of the package:
require("devtools")
devtools::install_github("hyunnaye/IsoformVisRNA", build_vignettes = TRUE)
library("IsoformVisRNA")To run the Shiny app:
IsoformVisRNA::runIsoformVisRNA()ls("package:IsoformVisRNA")
data(package = "IsoformVisRNA")
browseVignettes("IsoformVisRNA")
IsoformVisRNA contains 5 functions to analyze the alternative splicing
for the desired gene in samples. The combineCM function combines all
kallisto count matrices to a single data frame. The calculateRatios
function calculates the expression ratios for the two given transcript
ids. Below is a flowchart demonstate the workflow of this package. The
runIsoformVisRNA function can be used to launch the shiny app for this
package.
The author of the package is Nayeon Hyun. The combineCM function uses
the tools package to remove extensions from filenames to generate the
column names. The calculateRatios function makes use of the dplyr R
package to filter and retrieve the counts for the desired transcript
ids. The generateBarPlot function makes use of the ggplot2 R package
to generate its bar plot. The generateBarPlot function makes use of
the ggboxplot function in the ggpubr R package to generate its box
plot. This function also uses the stringr package to wrap the labels
to multiple lines in order to avoid overflowing labels.
ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 2012 Sep 6;489(7414):57-74. PMID: 22955616
Grolemund, G. (2015). Learn Shiny - Video Tutorials. https://shiny.rstudio.com/tutorial/
H. Wickham. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York, 2016.
Kassambara A (2023). ggpubr: ‘ggplot2’ Based Publication Ready Plots. R package version 0.6.0, https://CRAN.R-project.org/package=ggpubr.
R Core Team (2023). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/.
Wickham H (2022). stringr: Simple, Consistent Wrappers for Common String Operations. R package version 1.5.0, https://CRAN.R-project.org/package=stringr.
Wickham H, François R, Henry L, Müller K, Vaughan D (2023). dplyr: A Grammar of Data Manipulation. R package version 1.1.3, https://CRAN.R-project.org/package=dplyr.
This package was developed as part of an assessment for 2023 BCB410H:
Applied Bioinformatics course at the University of Toronto, Toronto,
CANADA. IsoformVisRNA welcomes issues, enhancement requests, and other
contributions. To submit an issue, use the GitHub
issues. Many thanks
to those who provided feedback to improve this package.
The package tree structure is provided below.
- IsoformVisRNA
|- IsoformVisRNA.Rproj
|- DESCRIPTION
|- NAMESPACE
|- LICENSE
|- README
|- data
|- Experiment_info.rda
|- Normalized_CM.rda
|- inst
|- CITATION
|- extdata
|- barplot.png
|- boxplot.png
|- flowchart.png
|- ratioDF.csv
|- shiny-scripts
|- app.R
|- man
|- calculateRatios.Rd
|- combineCounts.Rd
|- Experiment_info.Rd
|- generateBarPlot.Rd
|- generateBoxPlot.Rd
|- Normalized_CM.Rd
|- runIsoformVisRNA.Rd
|- R
|- combineCM.R
|- compare_expression.R
|- runIsoformVisRNA.R
|- tests
|- testthat.R
|- testthat
|- test-calculateRatios.R
|- test-generateBarPlot.R
|- test-generateBoxPlot.R
|- vignettes
|- Introduction_IsoformVisRNA.Rmd