snapmine Package Summary

snapmine enables querying junction inclusion of cryptic exons or other junctions of interest in bulk. Its initial use is described in the manuscript Large-scale RNA-seq mining reveals ciclopirox triggers TDP-43 cryptic exons which was published in Nature Communications.

Installation

Please install this package using remotes.

install.packages("remotes")
library(remotes)

remotes::install_github("irikas/snapmine")
library(snapmine)

Usage

An introductory vignette on how to use this package can be found within the “vignettes” directory. Using GitHub & BitBucket HTML Preview, you can also view it here.

For querying only a few junctions, it may be easier to use the online interface.

Algorithm

Below is Figure 1 from the publication. 1A is a schematic of the SnapMine algorithm.