Genotyping Uncertainty with Sequencing data - Base package
An R package for the basis of performing analysis on high-throughput sequencing data for a number of R packages, namely:
The novelty of these packages is the methods account for errors associated with low sequencing depth and miscalled bases, so that filtering with respect to read depth is not required.
The easiest way to install GUSbase in R is using the devtools package.
install.packages("devtools")
devtools::install_github("tpbilton/GUSbase")
Note: Some of the functions are coded in C and therefore an appropriate C compiler is needed for the package to work. For windows OS, Rtools (https://cran.r-project.org/bin/windows/Rtools/) provides a compiler.
GUSbase is Copyright 2017-2024 Timothy P. Bilton, released under the GNU General Public License version 3.
The initial development of this package was partially funed by the Ministry of Business, Innovation and Employment via its funding of the “Genomics for Production & Security in a Biological Economy” programme (Contract ID C10X1306).