Package: SBGNview 1.27.0

Weijun Luo

SBGNview: "SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"

SBGNview is a tool set for pathway based data visalization, integration and analysis. SBGNview is similar and complementary to the widely used Pathview, with the following key features: 1. Pathway definition by the widely adopted Systems Biology Graphical Notation (SBGN); 2. Supports multiple major pathway databases beyond KEGG (Reactome, MetaCyc, SMPDB, PANTHER, METACROP) and user defined pathways; 3. Covers 5,200 reference pathways and over 3,000 species by default; 4. Extensive graphics controls, including glyph and edge attributes, graph layout and sub-pathway highlight; 5. SBGN pathway data manipulation, processing, extraction and analysis.

Authors:Xiaoxi Dong*, Kovidh Vegesna*, Weijun Luo

SBGNview_1.27.0.tar.gz
SBGNview_1.27.0.zip(r-4.7)SBGNview_1.27.0.zip(r-4.6)SBGNview_1.27.0.zip(r-4.5)
SBGNview_1.27.0.tgz(r-4.6-any)SBGNview_1.27.0.tgz(r-4.5-any)
SBGNview_1.27.0.tar.gz(r-4.7-any)SBGNview_1.27.0.tar.gz(r-4.6-any)
SBGNview_1.27.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
SBGNview/json (API)
NEWS

# Install 'SBGNview' in R:
install.packages('SBGNview', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/datapplab/sbgnview/issues

Datasets:

On BioConductor:SBGNview-1.27.0(bioc 3.24)SBGNview-1.26.0(bioc 3.23)

genetargetpathwaysgraphandnetworkvisualizationgenesetenrichmentdifferentialexpressiongeneexpressionmicroarrayrnaseqgeneticsmetabolomicsproteomicssystemsbiologysequencing

6.39 score 29 stars 28 scripts 526 downloads 14 exports 77 dependencies

Last updated from:afcc5fe340. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR233
linux-devel-x86_64NOTE424
source / vignettesOK337
linux-release-x86_64NOTE439
macos-release-arm64NOTE307
macos-oldrel-arm64NOTE241
windows-develNOTE672
windows-releaseNOTE323
windows-oldrelNOTE667
wasm-releaseOK165

Exports:changeDataIdchangeIdsdownloadSbgnFilefindPathwayshighlightArcshighlightNodeshighlightPathloadMappingTableoutputFileoutputFile<-renderSbgnsbgn.gsetssbgnNodesSBGNview

Dependencies:abindAnnotationDbiaskpassbase64encBiobaseBiocGenericsBiostringsbitbit64bitopsblobbookdownbslibcachemclicpp11crayoncurlDBIDelayedArraydigestevaluatefastmapfontawesomefsgenericsGenomicRangesgluegraphhighrhtmltoolshttrigraphIRangesjquerylibjsonliteKEGGgraphKEGGRESTknitrlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslorg.Hs.eg.dbpathviewpkgconfigpngR6rappdirsrbibutilsRCurlRdpackRgraphvizrlangrmarkdownRSQLitersvgS4ArraysS4VectorssassSBGNview.dataSeqinfoSparseArraySummarizedExperimentsystinytexvctrsxfunXMLxml2XVectoryaml

SBGNview Based Pathway Analysis and Visualization Workflow

Xiaoxi Dong, Kovidh Vegesna, kvegesna (AT) uncc.edu, Weijun Luo, luo_weijun (AT) yahoo.com

Rendered frompathway.enrichment.analysis.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2021-03-03
Started: 2019-05-28

SBGNview Quick Start

Kovidh Vegesna, kvegesna (AT) uncc.edu, Weijun Luo, luo_weijun (AT) yahoo.com

Rendered fromSBGNview.quick.start.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2021-02-27
Started: 2021-02-25

SBGNview: Data Analysis, Integration and Visualization on Massive SBGN Pathway Collections

Xiaoxi Dong, Kovidh Vegesna, kvegesna (AT) uncc.edu, Weijun Luo, luo_weijun (AT) yahoo.com

Rendered fromSBGNview.Vignette.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2021-02-25
Started: 2019-05-28