The recommended way to install the eRNAkit package (including eRNAkitApp, small embeded data and associated workflows) is:
devtools::install_github("AneneLab/eRNAkit")
Most dependencies will be installed automatically. If any are missing, install them manually:
install.packages(c("tidyr", "dplyr", "ggplot2", "igraph", "data.table", "rintrojs", "shiny"))BiocManager::install("GenomicRanges")
The first launch of eRNAkitApp will also attempt to install any missing packages automatically.
Documentation for all implemented functions is available through the package, or here.
The complete reference database (see Core) is provided in the repository as eRNAkitDB.rds.
A high-confidence subset required by eRNAkitApp is bundled with the package installation.
Standard bioinformatics file formats, including BED, GTF, and FASTA, can be generated directly from eRNAkitDB using the package's utility functions. These utilities automatically export annotations for use with tools such as IGV, HTSeq-count, and bedtools.
See Core for additional details.