Package: SBGNview 1.21.0

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_1.21.0.tar.gz
SBGNview_1.21.0.zip(r-4.5)SBGNview_1.21.0.zip(r-4.4)SBGNview_1.21.0.zip(r-4.3)
SBGNview_1.21.0.tgz(r-4.4-any)SBGNview_1.21.0.tgz(r-4.3-any)
SBGNview_1.21.0.tar.gz(r-4.5-noble)SBGNview_1.21.0.tar.gz(r-4.4-noble)
SBGNview_1.21.0.tgz(r-4.4-emscripten)SBGNview_1.21.0.tgz(r-4.3-emscripten)
SBGNview.pdf |SBGNview.html✨
SBGNview/json (API)
NEWS

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

Peer review:

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

Datasets:

On BioConductor:SBGNview-1.21.0(bioc 3.21)SBGNview-1.20.0(bioc 3.20)

genetargetpathwaysgraphandnetworkvisualizationgenesetenrichmentdifferentialexpressiongeneexpressionmicroarrayrnaseqgeneticsmetabolomicsproteomicssystemsbiologysequencing

6.22 score 25 stars 22 scripts 374 downloads 14 exports 81 dependencies

Last updated 2 months agofrom:248ac8b2a1. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 19 2024
R-4.5-winNOTEDec 19 2024
R-4.5-linuxNOTEDec 19 2024
R-4.4-winNOTEDec 19 2024
R-4.4-macNOTEDec 19 2024
R-4.3-winNOTEDec 19 2024
R-4.3-macNOTEDec 19 2024

Exports:changeDataIdchangeIdsdownloadSbgnFilefindPathwayshighlightArcshighlightNodeshighlightPathloadMappingTableoutputFileoutputFile<-renderSbgnsbgn.gsetssbgnNodesSBGNview

Dependencies:abindAnnotationDbiaskpassbase64encBiobaseBiocGenericsBiostringsbitbit64bitopsblobbookdownbslibcachemclicpp11crayoncurlDBIDelayedArraydigestevaluatefastmapfontawesomefsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluegraphhighrhtmltoolshttrigraphIRangesjquerylibjsonliteKEGGgraphKEGGRESTknitrlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslorg.Hs.eg.dbpathviewpkgconfigplogrpngR6rappdirsrbibutilsRCurlRdpackRgraphvizrlangrmarkdownRSQLitersvgS4ArraysS4VectorssassSBGNview.dataSparseArraySummarizedExperimentsystinytexUCSC.utilsvctrsxfunXMLxml2XVectoryamlzlibbioc

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 Dec 19 2024.

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 Dec 19 2024.

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 Dec 19 2024.

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