Package: NetSAM 1.47.0
Zhiao Shi
NetSAM: Network Seriation And Modularization
The NetSAM (Network Seriation and Modularization) package takes an edge-list representation of a weighted or unweighted network as an input, performs network seriation and modularization analysis, and generates as files that can be used as an input for the one-dimensional network visualization tool NetGestalt (http://www.netgestalt.org) or other network analysis. The NetSAM package can also generate correlation network (e.g. co-expression network) based on the input matrix data, perform seriation and modularization analysis for the correlation network and calculate the associations between the sample features and modules or identify the associated GO terms for the modules.
Authors:
NetSAM_1.47.0.tar.gz
NetSAM_1.47.0.zip(r-4.5)NetSAM_1.47.0.zip(r-4.4)NetSAM_1.47.0.zip(r-4.3)
NetSAM_1.47.0.tgz(r-4.5-any)NetSAM_1.47.0.tgz(r-4.4-any)NetSAM_1.47.0.tgz(r-4.3-any)
NetSAM_1.47.0.tar.gz(r-4.5-noble)NetSAM_1.47.0.tar.gz(r-4.4-noble)
NetSAM_1.47.0.tgz(r-4.4-emscripten)NetSAM_1.47.0.tgz(r-4.3-emscripten)
NetSAM.pdf |NetSAM.html✨
NetSAM/json (API)
| # Install 'NetSAM' in R: |
| install.packages('NetSAM', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- netsam_output - An example of the list object returned by NetSAM function
On BioConductor:NetSAM-1.47.0(bioc 3.21)NetSAM-1.46.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 4 months agofrom:c829ddb9aa. Checks:1 OK, 7 ERROR. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Feb 16 2025 |
| R-4.5-win | ERROR | Feb 16 2025 |
| R-4.5-mac | ERROR | Feb 16 2025 |
| R-4.5-linux | ERROR | Feb 16 2025 |
| R-4.4-win | ERROR | Feb 16 2025 |
| R-4.4-mac | ERROR | Feb 16 2025 |
| R-4.3-win | ERROR | Feb 16 2025 |
| R-4.3-mac | ERROR | Feb 16 2025 |
Exports:consensusNetfeatureAssociationGOAssociationmapToSymbolMatNetMatSAMmergeDuplicateNetAnalyzerNetSAMtestFileFormat
Dependencies:AnnotationDbiaskpassbackportsbase64encBiobaseBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64blobbslibcacachemcheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrdigestdoParalleldplyrdynamicTreeCutevaluatefansifarverfastclusterfastmapfilelockfontawesomeforeachforeignFormulafsgclusgenericsGenomeInfoDbGenomeInfoDbDataggplot2glueGO.dbgridExtragtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2igraphimputeIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglatticelifecyclemagrittrMASSMatrixmatrixStatsmemoisemgcvmimemunsellnlmennetopensslpermutepillarpkgconfigplogrpngpreprocessCoreprettyunitsprogresspurrrqapR2HTMLR6rappdirsRColorBrewerRcppregistryrlangrmarkdownrpartRSQLiterstudioapiS4VectorssassscalesseriationstringistringrsurvivalsystibbletidyrtidyselecttinytexTSPUCSC.utilsutf8vctrsveganviridisviridisLiteWGCNAwithrxfunxml2XVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Network Seriation and Modularization | NetSAM-package |
| Construction of a consensus coexpression network | consensusNet |
| Calculate the associations between modules and sample features | featureAssociation |
| Identify the associated GO terms for each module | GOAssociation |
| Map other ids to gene symbols | mapToSymbol |
| Construction of correlation network from a matrix | MatNet |
| Correlation network construction, seriation and modularization from a matrix | MatSAM |
| Merge the duplicate Ids in the matrix data | mergeDuplicate |
| Network analyzer | NetAnalyzer |
| Network Seriation and Modularization | NetSAM |
| An example of the list object returned by NetSAM function | netsam_output |
| Test whether the data matrix and the annotation have a correct format | testFileFormat |
