Package: SGCP 1.7.0
SGCP: SGCP: A semi-supervised pipeline for gene clustering using self-training approach in gene co-expression networks
SGC is a semi-supervised pipeline for gene clustering in gene co-expression networks. SGC consists of multiple novel steps that enable the computation of highly enriched modules in an unsupervised manner. But unlike all existing frameworks, it further incorporates a novel step that leverages Gene Ontology information in a semi-supervised clustering method that further improves the quality of the computed modules.
Authors:
SGCP_1.7.0.tar.gz
SGCP_1.7.0.zip(r-4.5)SGCP_1.7.0.zip(r-4.4)SGCP_1.7.0.zip(r-4.3)
SGCP_1.7.0.tgz(r-4.4-any)SGCP_1.7.0.tgz(r-4.3-any)
SGCP_1.7.0.tar.gz(r-4.5-noble)SGCP_1.7.0.tar.gz(r-4.4-noble)
SGCP_1.7.0.tgz(r-4.4-emscripten)SGCP_1.7.0.tgz(r-4.3-emscripten)
SGCP.pdf |SGCP.html✨
SGCP/json (API)
NEWS
# Install 'SGCP' in R: |
install.packages('SGCP', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/na396/sgcp/issues
- cheng - Normalized gene expression data from Cheng et al.'s publication on ischemic cardiomyopathy (ICM).
- resClus - An example of the output from 'clustering' function in the SGCP pipeline
- resFinalGO - An example of the output from 'geneOntololgy' function in the SGCP pipeline
- resInitialGO - An example of the output from the 'geneOntololgy' function in the SGCP pipeline
- resSemiLabel - An example of the output from 'semiLabeling' function in the SGCP pipeline
- resSemiSupervised - An example of the output from 'semiSupervised' function in the SGCP pipeline
- sgcp - An example of the output of 'ezSGCP' function in the SGCP pipeline
On BioConductor:SGCP-1.7.0(bioc 3.21)SGCP-1.6.0(bioc 3.20)
geneexpressiongenesetenrichmentnetworkenrichmentsystemsbiologyclassificationclusteringdimensionreductiongraphandnetworkneuralnetworknetworkmrnamicroarrayrnaseqvisualizationbioinformaticsgenecoexpressionnetworkgraphsnetworkclusteringnetworksself-trainingsemi-supervised-learningunsupervised-learning
Last updated 23 days agofrom:ba0ddcc40f. Checks:OK: 1 WARNING: 6. Indexed: yes.
Target | Result | Date |
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Doc / Vignettes | OK | Nov 18 2024 |
R-4.5-win | WARNING | Nov 18 2024 |
R-4.5-linux | WARNING | Nov 18 2024 |
R-4.4-win | WARNING | Nov 18 2024 |
R-4.4-mac | WARNING | Nov 18 2024 |
R-4.3-win | WARNING | Nov 18 2024 |
R-4.3-mac | WARNING | Nov 18 2024 |
Exports:adjacencyMatrixclusteringezSGCPgeneOntologysemiLabelingsemiSupervisedSGCP_ezPLOTSGCP_plot_barSGCP_plot_conductanceSGCP_plot_densitySGCP_plot_heatMapSGCP_plot_jitterSGCP_plot_pcaSGCP_plot_pieSGCP_plot_silhouette
Dependencies:abindannotateAnnotationDbiAnnotationForgeaskpassBHBiobaseBiocGenericsBiostringsbitbit64bitopsblobbootcachemcaretCategorycellrangerclassclicliprclockcodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArrayDescToolsdiagramdigestdplyre1071Exactexpmfansifarverfastmapforcatsforeachfuturefuture.applygenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggridgesgldglobalsglueGO.dbGOstatsgowergraphGSEABasegtablehardhathavenhmshttripredIRangesisobanditeratorsjsonliteKEGGRESTKernSmoothlabelinglatticelavalifecyclelistenvlmomlubridatemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeModelMetricsmunsellmvtnormnlmennetnumDerivopensslopenxlsxorg.Hs.eg.dbparallellypillarpkgconfigplogrplyrpngprettyunitspROCprodlimprogressprogressrproxypurrrR6RBGLRColorBrewerRcppRcppEigenRCurlreadrreadxlrecipesrematchreshape2RgraphvizrlangrootSolverpartRSpectraRSQLiterstudioapiS4ArraysS4VectorsscalesshapeSparseArraySQUAREMstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttimechangetimeDatetzdbUCSC.utilsutf8vctrsviridisLitevroomwithrXMLxtableXVectorzipzlibbioc