shiny.effectR

Local path of folder containing the MAFFT binary executable file or the executable file itself. If not specified, then MAFFT must be in the program search path.

mafft.path

Local path of folder containing the HMMER binaries. If not specified, then HMMER executables must be in the program search path.

hmm.path

This function will launch an interactive web interface to run the effectR package functions to obtain effectors. It runs using the shiny R package.

Predicts cytoplasmic effector proteins using genomic data by searching for motifs of interest using regular expression searches and hidden Markov models (HMM) based in Haas et al. (2009) <doi:10.1038/nature08358>.

shiny.effectR: Function to run the effectR package using a shiny app

Description

Usage

Arguments

Details