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✨
DESCRIPTION |NEWS
card.svg |card.png
SBGNview/json (API)

# 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

6.43 score 29 stars 31 scripts 14 exports 77 dependencies

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

TargetResultTimeFilesSyslog
bioc-checksERROR239
linux-devel-x86_64NOTE424
source / vignettesOK343
linux-release-x86_64NOTE419
macos-release-arm64NOTE295
macos-oldrel-arm64NOTE206
windows-develNOTE342
windows-releaseNOTE306
windows-oldrelNOTE330
wasm-releaseOK172

Exports:changeDataIdchangeIdsdownloadSbgnFilefindPathwayshighlightArcshighlightNodeshighlightPathloadMappingTableoutputFileoutputFile<-renderSbgnsbgn.gsetssbgnNodesSBGNview

Dependencies:abindAnnotationDbiaskpassbase64encBiobaseBiocGenericsBiostringsbitbit64bitopsblobbookdownbslibcachemclicpp11crayoncurlDBIDelayedArraydigestevaluatefastmapfontawesomefsgenericsGenomicRangesgluegraphhighrhtmltoolshttrigraphIRangesjquerylibjsonliteKEGGgraphKEGGRESTknitrlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslorg.Hs.eg.dbpathviewpkgconfigpngR6rappdirsrbibutilsRCurlRdpackRgraphvizrlangrmarkdownRSQLitersvgS4ArraysS4VectorssassSBGNview.dataSeqinfoSparseArraySummarizedExperimentsystinytexvctrsxfunXMLxml2XVectoryaml

SBGNview Based Pathway Analysis and Visualization Workflow
Introduction | Citation | Installation and quick start | Complete pathway analysis + visualization workflow | Load the gene (RNA-seq) data | Gene sets from SBGNview pathway collection | Load gene set for mouse with ENSEMBL gene IDs | Pathway or gene set analysis using GAGE | Visualize perturbations in top SBGN pathways | Calculate fold changes or gene perturbations | Visualize pathway perturbations by SBNGview | SBGNview with SummarizedExperiment object | Session Info
Rendered frompathway.enrichment.analysis.Rmdusingknitr::rmarkdown

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

SBGNview Quick Start
Overview | Citation | Installation | Prerequisites | Install SBGNview | Quick example | Additional information | Session Info
Rendered fromSBGNview.quick.start.Rmdusingknitr::rmarkdown

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

SBGNview: Data Analysis, Integration and Visualization on Massive SBGN Pathway Collections
Overview | Citation | Installation and quick start | Getting started | Load the SBGNview package, together with pathview and other dependencies | Accessing help and documentation | SBGN pathway file (SBGN-ML) | Two tiers of support and two scenarios with SBGN based pathways | Load SBGNview's SBGN-ML pathway data collection | Information about the SBGN-ML pathway data collection | Search for pathways by keywords | Different layout for the same pathway | Custom SBGN-ML files | Basic visualization | Visualize gene data | Visualize compound data | Visualize both gene data and compound data | Work with SBGNview object | Structure of SBGNview object | Extract glyphs and arcs infromation from SBGNview object | Modify SBGNview object directly | Change output file name and format of SBGNview objects | Updating & modifying graphs | Hightlight nodes | Highlight all nodes | Highlight nodes by class | Show node IDs instead of node labels | Adjust node labels. | Label position, font size, color, change labels | Label text wrapping into multiple lines | When one input ID maps to multiple nodes | Highlight arcs and paths | Different layouts for the same pathway | SVG Editing Tool | ID mapping | Map between two types of IDs | Extract molecule list from pathways | Example using selected database | Use Reactome pathway database | Test SBGN reference cards | FAQs | Color key | Turn off color key | Session Info | References
Rendered fromSBGNview.Vignette.Rmdusingknitr::rmarkdown

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