,
Pemra Ozbek Sarica [aut],
Kazim Yalcin Arga [aut]| Title: | Identification of Tumor-Discriminating mRNA Signatures via Support Vector Machines Supported by Disease Ontology |
|---|---|
| Description: | It is an easy-to-use GUI using disease information for detecting tumor/normal sample discriminating gene sets from differentially expressed genes. Our approach is based on an iterative algorithm filtering genes with disease ontology enrichment analysis and wilk and wilks lambda criterion connected to SVM classification model construction. Along with gene set extraction, SVMDO also provides individual prognostic marker detection. The algorithm is designed for FPKM and RPKM normalized RNA-Seq transcriptome datasets. |
| Authors: | Mustafa Erhan Ozer [aut, cre] ,
Pemra Ozbek Sarica [aut],
Kazim Yalcin Arga [aut] |
| Maintainer: | Mustafa Erhan Ozer <[email protected]> |
| License: | GPL-3 |
| Version: | 1.5.5 |
| Built: | 2024-09-30 05:54:10 UTC |
| Source: | https://github.com/bioc/SVMDO |
SVMDO
innerServer_7(input, output, session)innerServer_7(input, output, session)
input |
server input |
output |
server output |
session |
server session |
Server section of wilks lambda filtration and SVM classification of disease filtered differentially expressed gene set
SVMDO
innerUI_classification(id)innerUI_classification(id)
id |
connection input |
UI section of wilks lambda filtration and SVM classification of disease filtered differentially expressed gene set
SVMDO
innerServer_clinic(input, output, session)innerServer_clinic(input, output, session)
input |
server input |
output |
server output |
session |
server session |
Server section of loading clinical data
SVMDO
innerUI_clinic_data(id)innerUI_clinic_data(id)
id |
connection input |
UI section of loading clinical data
SVMDO
innerServer_3(input, output, session, rawData, rval)innerServer_3(input, output, session, rawData, rval)
input |
server input |
output |
server output |
session |
server session |
rawData |
expression dataset provided from innerServer_exp_server |
rval |
Selected radio button information provided from innerServer_rad_server |
Server section of differential gene expression analysis
SVMDO
innerUI_deg_analysis(id)innerUI_deg_analysis(id)
id |
connection input |
UI section of differential gene expression analysis
SVMDO
disc_gene_download_ui(id)disc_gene_download_ui(id)
id |
connection input |
UI section of discriminative gene set download button
SVMDO
disc_gene_dw_server(input, output, session, gene_list_val)disc_gene_dw_server(input, output, session, gene_list_val)
input |
server input |
output |
server output |
session |
server session |
gene_list_val |
discriminative gene set list variable |
Server section of discriminative gene set download button
SVMDO
innerServer_6(input, output, session)innerServer_6(input, output, session)
input |
server input |
output |
server output |
session |
server session |
Server section of disease ontology based filtration of differentially expressed genes
SVMDO
innerUI_disease_ont_class(id)innerUI_disease_ont_class(id)
id |
connection input |
UI section of disease ontology based filtration of differentially expressed genes
SVMDO
innerServer_exp(input, output, session)innerServer_exp(input, output, session)
input |
server input |
output |
server output |
session |
server session |
Server section of providing expression dataset
SVMDO
innerServer(input, output, session)innerServer(input, output, session)
input |
server input |
output |
server output |
session |
server session |
Server section of entering output/working for gene list directory
SVMDO
innerUI_path(id)innerUI_path(id)
id |
connection input |
UI section of entering output/working for gene list directory
SVMDO
innerServer_10(input, output, session)innerServer_10(input, output, session)
input |
server input |
output |
server output |
session |
server session |
Server section of entering final gene list name
SVMDO
innerUI_gene_names(id)innerUI_gene_names(id)
id |
connection input |
UI section of entering top gene value
SVMDO
deg_data_table_ui(id)deg_data_table_ui(id)
id |
connection input |
Providing table form of discriminative gene sets in GUI
SVMDO
Including script files and global variables of GUI required to be initiated at the runApp file execution
SVMDO
innerServer_9(input, output, session)innerServer_9(input, output, session)
input |
server input |
output |
server output |
session |
server session |
Server section of workspace clearance
SVMDO
innerUI_clear_env(id)innerUI_clear_env(id)
id |
connection input |
UI section of workspace clearance
SVMDO
innerUI_exp_data(id)innerUI_exp_data(id)
id |
connection input |
UI section of providing expression dataset into GUI
SVMDO
plot_list_server(input, output, session)plot_list_server(input, output, session)
input |
server input |
output |
server output |
session |
server session |
Server section of preparing plot list to be visualized in GUI page
SVMDO
innerUI_collect_plot_data(id)innerUI_collect_plot_data(id)
id |
connection output |
UI section of preparing plot list to be visualized in GUI page
SVMDO
plot_push_server(input, output, session)plot_push_server(input, output, session)
input |
server input |
output |
server output |
session |
server session |
Server section of providing information about total number of survival plots for visualization
SVMDO
innerUI_plot_inject(id)innerUI_plot_inject(id)
id |
connection input |
UI section of providing information about total number of survival plots for visualization
SVMDO
plot_show_server(input, output, session, max_data)plot_show_server(input, output, session, max_data)
input |
server input |
output |
server output |
session |
server session |
max_data |
Information of total number of survival plots prepared with discriminative gene set |
Server section of providing information about total number of survival plots for visualization
SVMDO
innerUI_plot_show(id)innerUI_plot_show(id)
id |
connection input |
UI section of providing information about total number of survival plots for visualization
SVMDO
linebreaks(n)linebreaks(n)
n |
linebreak function variable |
Returning GUI window screen
#SVMDO::runGUI() Calling GUI without activating library #runGUI() Calling GUI after activating library # Disease Ontology Enrichment of a differentially expresed gene (entrez id): a_1<-DOSE::enrichDO(2981,ont="HDO")#SVMDO::runGUI() Calling GUI without activating library #runGUI() Calling GUI after activating library # Disease Ontology Enrichment of a differentially expresed gene (entrez id): a_1<-DOSE::enrichDO(2981,ont="HDO")
SVMDO
surv_plot_dw_server(input, output, session)surv_plot_dw_server(input, output, session)
input |
server input |
output |
server output |
session |
server session |
Server section of downloading survival plots of discriminative gene set
SVMDO
surv_plots_download_ui(id)surv_plots_download_ui(id)
id |
connection input |
UI section of downloading survival plots of discriminative gene set
SVMDO
innerServer_8(input, output, session, rawData_2, rval)innerServer_8(input, output, session, rawData_2, rval)
input |
server input |
output |
server output |
session |
server session |
rawData_2 |
Clinical data provided from clinic_data_input_server |
rval |
Selected radio button information provided from innerServer_rad_server |
Server section of survival analysis of final discriminative gene set
SVMDO
innerUI_surv(id)innerUI_surv(id)
id |
connection input |
UI section of survival analysis of final discriminative gene set
SVMDO
table_server(input, output, session)table_server(input, output, session)
input |
server input |
output |
server output |
session |
server session |
Server section of providing discriminative gene set for preparing table
SVMDO
innerUI_table_show(id)innerUI_table_show(id)
id |
connection input |
UI section of providing discriminative gene set for preparing table
SVMDO
innerServer_rad(input, output, session)innerServer_rad(input, output, session)
input |
server input |
output |
server output |
session |
server session |
Server section of providing information about selected radio button
SVMDO
innerUI_test_data(id)innerUI_test_data(id)
id |
connection input |
UI section of providing information about selected radio button
SVMDO
innerServer_5(input, output, session, top_val)innerServer_5(input, output, session, top_val)
input |
server input |
output |
server output |
session |
server session |
top_val |
top gene number value provided from top_val_server |
Server section of selecting differentially expressed genes based on top gene value
SVMDO
innerUI_top_gene_selection(id)innerUI_top_gene_selection(id)
id |
connection input |
UI section of selecting differentially expressed genes based on top gene value
SVMDO
innerServer_4(input, output, session)innerServer_4(input, output, session)
input |
server input |
output |
server output |
session |
server session |
Server section of entering top gene value
SVMDO
innerUI_top_gene_val(id)innerUI_top_gene_val(id)
id |
connection input |
UI section of entering top gene value