ClaidentTutorial

Tutorial scripts and data for Claident.

Prerequisites to run 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.

Prerequisites to run analyses in R

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())

Prerequisites to learn about Claident and R

Just download this package and extract to working directory.

Learning how to run Claident

See the following shell scripts, inputs and outputs.

runClaident_singleend.sh
runClaident_overlappedpairedend.sh
runClaident_nonoverlappedpairedend.sh
runClaident_overlappedpairedend_wSTD.sh

Learning how to analyze Claident outputs in R

See the following R codes, inputs and outputs.

runR_overlappedpairedend.R
runR_overlappedpairedend_wSTD.R