文件列表:

LICENSE (35149, 2023-10-19)
VIRIDIC/ (0, 2023-10-19)
VIRIDIC/functions.R (1520, 2023-10-19)
VIRIDIC/server.R (26745, 2023-10-19)
VIRIDIC/stand_alone/ (0, 2023-10-19)
VIRIDIC/stand_alone/Checker_data/ (0, 2023-10-19)
VIRIDIC/stand_alone/Checker_data/TestSet_ViridiMs_Heatmap.fasta (1141076, 2023-10-19)
VIRIDIC/stand_alone/Checker_data/TestSet_ViridiMs_Heatmap_reversed_permuted.fasta (1295573, 2023-10-19)
VIRIDIC/stand_alone/Checker_data/all_zobellviridae_genomes_input.fasta (581040, 2023-10-19)
VIRIDIC/stand_alone/Checker_data/four_very_short_zobellviridae_genomes_input.fasta (18559, 2023-10-19)
VIRIDIC/stand_alone/download/ (0, 2023-10-19)
VIRIDIC/stand_alone/download/viridic_manual_v1.1.pdf (553932, 2023-10-19)
VIRIDIC/stand_alone/user-install/ (0, 2023-10-19)
VIRIDIC/stand_alone/user-install/How to use VIRIDIC.txt (1890, 2023-10-19)
VIRIDIC/stand_alone/user-install/VIRIDIC.yml (5672, 2023-10-19)
VIRIDIC/stand_alone/viridic_scripts/ (0, 2023-10-19)
VIRIDIC/stand_alone/viridic_scripts/00_viridic_master.R (24636, 2023-10-19)
VIRIDIC/stand_alone/viridic_scripts/01_VIRIDIC_sim_calc.R (12184, 2023-10-19)
VIRIDIC/stand_alone/viridic_scripts/02_viridic_cluster.R (7557, 2023-10-19)
VIRIDIC/stand_alone/viridic_scripts/03_viridic_heatmap.R (16985, 2023-10-19)
VIRIDIC/stand_alone/viridic_scripts/VIRIDIC_functions.R (3069, 2023-10-19)
VIRIDIC/stand_alone/viridic_scripts/viridic_checker.R (4731, 2023-10-19)
VIRIDIC/stand_alone/viridic_scripts/viridic_manual_v1.1.txt (7366, 2023-10-19)
VIRIDIC/ui.R (36642, 2023-10-19)

# VIRIDIC VIRIDIC (Virus Intergenomic Distance Calculator) computes pairwise intergenomic distances/similarities amongst viral genomes. VIRIDIC is available at http://viridic.icbm.de as a web-service or a singularity package. In addition, the R language source code can be accessed from this repository. If you use VIRIDIC, please cite: Moraru, C., Varsani, A., and Kropinski, A.M. (2020) VIRIDIC – a novel tool to calculate the intergenomic similarities of prokaryote-infecting viruses. Viruses 12(11). https://doi.org/10.3390/v12111268 This repository contains: - the source code for the stand-alone VIRIDIC, written in R - the source code for the shiny-app, which provides a graphical user interface for the standa-alone VIRIDIC ## How to install VIRIDIC * copy to your profile the content of the VIRIDIC folder * create and activate the VIRIDIC conda env - use the yml file from /VIRIDIC/stand_alone/user-install/VIRIDIC.yml to create the VIRIDIC conda env - install the specific R libraries ```bash conda env create -f VIRIDIC.yml conda activate VIRIDIC ``` ### Install R libraries from within R ```bash R #this command starts R ``` ```R options(repos = c(CRAN = "https://cloud.r-project.org/")) install.packages("stringr") install.packages("magrittr") install.packages("dplyr") install.packages("tibble") install.packages("purrr") install.packages("tidyr") install.packages("ggplot2") install.packages("data.table") install.packages("DT") install.packages("shiny") install.packages("shinyjs") install.packages("shinyWidgets") install.packages("shinythemes") install.packages("seqinr") #install.packages("IRanges") if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("IRanges") install.packages("reshape2") install.packages("pheatmap") install.packages("fastcluster") install.packages("parallelDist") install.packages("furrr") install.packages("future") #install.packages("ComplexHeatmap") if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("ComplexHeatmap") ``` ## How to run VIRIDIC shiny-app * Open RStudio, create a new project for the folder VIRIDIC (directly in this folder there are the files of the shiny-app) * open either ui.R or server.R files in RStudio, press button "Run App" * this will start the VIRIDIC GUI, which then runs the VIRIDIC stand-alone code * In addition, if you install the shiny-server, you can run VIRIDIC as an independent web-app. ## How to run VIRIDIC stand-alone * go to your folder with the VIRIDIC scripts * use the command "Rscript 00_viridic_master.R [...options]" * for options, see manual, either by running "Rscript 00_viridic_master.R help" or by checking the PDF file here: /VIRIDIC/stand_alone/download/viridic_manual_v1.1.pdf ```R # example of how to run one VIRIDIC analysis Rscript 00_viridic_master.R projdir=/home/cmoraru/TEST_CLM/testVIridic in=/home/cmoraru/TEST_CLM/Ebeline_rel.fna ncor=10 ```

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