Tutorial scripts and data for Claident.
Claident, associated databases and programs need to be installed. Use ClaidentInstaller to install them. In addition, this package need to be downloaded and extracted to working directory.
R and several packages need to be installed. Install R, and then, execute the following command in R
library(parallel)
install.packages(c("vegan", "colorspace", "RColorBrewer", "tidyverse", "ggsci", "khroma", "picante", "bipartite", "geosphere", "foreach", "doParallel", "mpmcorrelogram", "pvclust"), repos="http://cloud.r-project.org/", dependencies=T, clean=T, Ncpus=detectCores())
Just download this package and extract to working directory.
See the following shell scripts, inputs and outputs.
- runClaident_singleend.sh
- runClaident_overlappedpairedend.sh
- runClaident_nonoverlappedpairedend.sh
- runClaident_overlappedpairedend_wSTD.sh
See the following R codes, inputs and outputs.