halfBaked is a collection of convenience functions to aid in `omics analyses. They span functions to automate and organize repetitive analyses (e.g. many pairwise RNA-seq comparisons) to viz.
More specifically, they’re designed to help create template Rmd notebooks to jumpstart exploratory data analysis and get the ball rolling for common data modalities.
These templates are provided as vignettes and can be accessed via the browseVignettes("halfBaked") function.
Installation
Get the latest stable R release from CRAN. Then install halfBaked from Github:
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("j-andrews7/halfBaked")Design Principles
halfBaked is intended to help save experienced bioinformaticians some time with relatively run of the mill analyses. It is not intended as an out of the box solution for bioinformatics newbies.
It is not recommended for use without a solid understanding of the underlying methods and assumptions.