This instruction will guide the users to use the circlncRNAnet in local mode. To set up a local run mode, the following three items are required:
- Linux environment.
- R, v3.3.2 is recommended.
- RStudio.
Then, follow the instructions below for installation and data analyses:
# download circlncRNAnet
git clone https://github.com/smw1414/circlncRNAnet.git
cd circlncRNAnet
# make all scripts executable
chmod +x *.[Rr]
chmod +x *.sh
# installation of reguired pakcages for R
R
install.packages(c("shiny","shinyjs","ggplot2","plotly","data.table","DT","visNetwork","googleVis","magrittr","factoextra","plyr","circlize","getopt"))
source("https://bioconductor.org/biocLite.R")
biocLite(c("DESeq2","BiocParallel","org.Hs.eg.db","clusterProfiler"))
q("no")
wget http://app.cgu.edu.tw/circlnc/db/db.zip # 1GB
wget http://app.cgu.edu.tw/circlnc/tcga/tcga.zip # 1.6GB
unzip db.zip
unzip tcga.zip
- Please refer http://app.cgu.edu.tw/circlnc/circlnc_tutorial/_book/data-input.html#preparation-of-input-files
- Open RStudio and create a new R project under the folder of circlncRNAnet.
- Run the following commands for either lncRNA or circRNA differential expression analyses.
# lncRNA
system("./lncrna_local_run_deg.sh <gene reads count table> <demographic table>")
# circRNA
system("./circrna_local_run_deg.sh <gene reads count table> <demographic table> <circRNA reads count table>")
# TCGA data
# Please refer the table below for the available TCGA datasets
system("./lncrna_local_run_deg_tcga.sh <cancer code>")
system("./lncrna_local_run_deg_tcga.sh TCGA-LUAD")
# example of demo datset
# lncRNA
system("./lncrna_local_run_deg.sh demo_file/TCGA_COADREAD_GENCODEV25_raw_read_count.txt demo_file/TCGA_COADREAD_GENCODEV25_condition.txt")
# circRNA
system("./circrna_local_run_deg.sh demo_file/encode_example_Gene_raw_read_count_casted.txt demo_file/encode_example_circRNA_condition.txt demo_file/encode_example_circRNA_raw_read_count_casted.txt ")
| TCGA datasets | |||
|---|---|---|---|
| TCGA-BLCA | TCGA-ESCA | TCGA-LIHC | TCGA-PRAD |
| TCGA-BRCA | TCGA-HNSC | TCGA-LUAD | TCGA-READ |
| TCGA-CESC | TCGA-KICH | TCGA-LUSC | TCGA-STAD |
| TCGA-CHOL | TCGA-KIRC | TCGA-PAAD | TCGA-THCA |
| TCGA-COAD | TCGA-KIRP | TCGA-PCPG | TCGA-UCEC |
-
Open the file browser in the right bottom panel.
-
Open the app.R under the deg folder for lncRNA or the degc folder for circRNA analysis.
-
Run the app by clicking Run App.
- Users can browse and select the gene of interest now.
- The Calcaulate co-expression button was designed for the PHP and the Shiny enviroment. Thus, the button is non-functional in this enviroment. To calculate the co-expressed genes, please follow the next step.
# lncRNA
system("./lncrna_local_run_cor.sh <lncRNAs>")
# circRNA
system("./circrna_local_run_cor.sh <circRNAs>")
# <lncRNAs/circRNAs> could be one or more genes, seperated by comma.
# example of demo datset
# lncRNA
system("./lncrna_local_run_cor.sh CCAT1,PVT1")
# circRNA
system("./circrna_local_run_cor.sh chr11_35204640_35201082_fwd,chr10_97437191_97438703_rev,chr9_128515639_128508876_fwd")
-
Open the file browser in the right bottom panel.
-
Open the app.R under the coexp folder for lncRNA or the coexpc folder for circRNA analysis.
-
Run the app by clicking Run App.
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