Installation and Package Loading | Introduction | Implementation | Dataset Preparation | SVMDO GUI Description | How to open SVMDO Main Screen | How to use SVMDO Main Screen | Steps of Analysis Screen | Steps of Result Screen | Application of test datasets | Workspace Clearance | Output Files of SVMDO | References | How to install R and RStudio GUI | Windows Operating System | Ubuntu Operating System | Session Info
Package: SVMDO 1.13.0
Mustafa Erhan Ozer
SVMDO: Identification of Tumor-Discriminating mRNA Signatures via Support Vector Machines Supported by Disease Ontology
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:
SVMDO_1.13.0.tar.gz
SVMDO_1.13.0.zip(r-4.7)SVMDO_1.13.0.zip(r-4.6)SVMDO_1.13.0.zip(r-4.5)
SVMDO_1.13.0.tgz(r-4.6-any)SVMDO_1.13.0.tgz(r-4.5-any)
SVMDO_1.13.0.tar.gz(r-4.7-any)SVMDO_1.13.0.tar.gz(r-4.6-any)
SVMDO_1.13.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SVMDO/json (API)
| # Install 'SVMDO' in R: |
| install.packages('SVMDO', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/robogeno/svmdo/issues
On BioConductor:SVMDO-1.13.0(bioc 3.24)SVMDO-1.11.0(bioc 3.23)
genesetenrichmentdifferentialexpressionguiclassificationrnaseqtranscriptomicssurvivalmachine-learningrna-seqshiny
Last updated from:44126c7924. Checks:1 NOTE, 7 ERROR, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 246 | ||
| linux-devel-x86_64 | ERROR | 492 | ||
| source / vignettes | OK | 309 | ||
| linux-release-x86_64 | ERROR | 419 | ||
| macos-release-arm64 | ERROR | 260 | ||
| macos-oldrel-arm64 | ERROR | 182 | ||
| windows-devel | ERROR | 311 | ||
| windows-release | ERROR | 284 | ||
| windows-oldrel | ERROR | 386 | ||
| wasm-release | OK | 233 |
Exports:runGUI
Dependencies:abindAnnotationDbiaskpassattemptbase64encBiobaseBiocGenericsBiostringsbitbit64bitopsblobBSDAbslibcachemcaretcaToolsclassclassIntclicliprclockcodetoolscombinatcommonmarkconfigcpp11crayoncrosstalkcurldata.tabledatawizardDBIDelayedArraydiagramdigestDOSEdplyrDTe1071enrichitevaluatefarverfastmapfontawesomeforcatsforeachfsfuturefuture.applygenericsGenomicRangesggplot2globalsglueGO.dbgolemGOSemSimgowergtablehardhathavenhighrhmshtmltoolshtmlwidgetshttpuvhttrinsightipredIRangesisobanditeratorsjquerylibjsonliteKEGGRESTKernSmoothklaRknitrlabelinglabelledlaterlatticelavalazyevallifecyclelistenvlubridatemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeminiUIModelMetricsnlmennetnortestnumDerivopensslorg.Hs.eg.dbotelparallellypillarpkgconfigplyrpngprettyunitspROCprodlimprogressprogressrpromisesproxypurrrquestionrR.cacheR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppEigenreadrrecipesreshape2rlangrmarkdownrpartrprojrootRSQLiterstudioapiS4ArraysS4VectorsS7sassscalesSeqinfoshapeshinyshinyFilesshinytitlesjlabelledsjmiscsourcetoolsSparseArraysparsevctrsSQUAREMstringistringrstylerSummarizedExperimentsurvivalsystibbletidyrtidyselecttimechangetimeDatetinytextzdbutf8vctrsviridisLitevroomwithrxfunxtableXVectoryamlyulab.utils
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| SVMDO | classification_server innerServer_7 |
| SVMDO | classification_ui innerUI_classification |
| SVMDO | clinic_data_input_server innerServer_clinic |
| SVMDO | clinic_data_input_ui innerUI_clinic_data |
| SVMDO | deg_server innerServer_3 |
| SVMDO | deg_ui innerUI_deg_analysis |
| SVMDO | disc_gene_download_ui |
| SVMDO | disc_gene_dw_server |
| SVMDO | do_based_gene_filtration_server innerServer_6 |
| SVMDO | do_based_gene_filtration_ui innerUI_disease_ont_class |
| SVMDO | expression_dataset_input_server innerServer_exp |
| SVMDO | gene_directory_selection_server innerServer |
| SVMDO | gene_directory_selection_ui innerUI_path |
| SVMDO | gene_list_name_server innerServer_10 |
| SVMDO | gene_list_name_ui innerUI_gene_names |
| SVMDO | deg_data_table_ui gene_list_table_visualization_ui |
| SVMDO | globals |
| SVMDO | gui_obj_removal_server innerServer_9 |
| SVMDO | gui_obj_removal_ui innerUI_clear_env |
| SVMDO | innerServer_exp_ui innerUI_exp_data |
| SVMDO | package_req_list |
| SVMDO | plot_list_server |
| SVMDO | innerUI_collect_plot_data plot_list_ui |
| SVMDO | plot_push_server |
| SVMDO | innerUI_plot_inject plot_push_ui |
| SVMDO | plot_show_server |
| SVMDO | innerUI_plot_show plot_show_ui |
| SVMDO | linebreaks runGUI |
| SVMDO | surv_plot_dw_server |
| SVMDO | surv_plots_download_ui surv_plot_dw_ui |
| SVMDO | innerServer_8 survival_analysis_server |
| SVMDO | innerUI_surv survival_analysis_ui |
| SVMDO | table_server |
| SVMDO | innerUI_table_show table_ui |
| SVMDO | innerServer_rad test_data_selection_server |
| SVMDO | innerUI_test_data test_data_selection_ui |
| SVMDO | innerServer_5 top_val_based_deg_filtration |
| SVMDO | innerUI_top_gene_selection top_val_based_deg_filtration_ui |
| SVMDO | innerServer_4 top_val_server |
| SVMDO | innerUI_top_gene_val top_val_ui |