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claidenttutorial

https://github.com/astanabe/claidenttutorial

Science Score: 26.0%

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    CITATION.cff file
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    Low similarity (8.0%) to scientific vocabulary
Last synced: 9 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: astanabe
  • License: gpl-2.0
  • Language: Shell
  • Default Branch: main
  • Size: 716 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created about 1 year ago · Last pushed about 1 year ago
Metadata Files
Readme License Citation

README.md

ClaidentTutorial

Tutorial scripts and data for Claident.

Lecture video is available

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. For wordcloud image generation ("clplotwordcloud" command), Google Chrome or Chromium is also required.

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/", clean=T, upgrade="never", Ncpus=detectCores())

You might need to install several programs and/or libraries such as libssl or libgdal before executing the above package installation in R. If you are trying to run this tutorial on Ubuntu or Debian, the following command may helps you.

sudo apt install libssl-dev libgdal-dev

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.

Learning how to analyze Claident outputs in R

See the following R codes, inputs and outputs.

Owner

  • Name: Akifumi S. Tanabe
  • Login: astanabe
  • Kind: user
  • Location: Sendai, Miyagi, Japan
  • Company: Graduate School of Life Sciences, Tohoku University

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