Package: SMITE 1.35.0

Neil Ari Wijetunga

SMITE: Significance-based Modules Integrating the Transcriptome and Epigenome

This package builds on the Epimods framework which facilitates finding weighted subnetworks ("modules") on Illumina Infinium 27k arrays using the SpinGlass algorithm, as implemented in the iGraph package. We have created a class of gene centric annotations associated with p-values and effect sizes and scores from any researchers prior statistical results to find functional modules.

Authors:Neil Ari Wijetunga, Andrew Damon Johnston, John Murray Greally

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SMITE.pdf |SMITE.html✨
SMITE/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/greallylab/smite/issues

Datasets:
  • REACTOME - An Igraph network for REACTOME with nodes as gene symbols
  • expression_curated - A toy dataset ofcurated RNA-seq to test within SMITE
  • genes - A small set of RefSeq genes for converting
  • h3k4me1 - A toy dataset of H3k4me1 peaks to test within SMITE
  • hg19_genes - A bed file annotating Refseq genes for the hg19 genome build
  • methylation - A toy dataset of DNA methylation to test within SMITE
  • test_annotation - A toy PvalueAnnotation

On BioConductor:SMITE-1.33.0(bioc 3.21)SMITE-1.34.0(bioc 3.20)

immunooncologydifferentialmethylationdifferentialexpressionsystemsbiologynetworkenrichmentgenomeannotationnetworksequencingrnaseqcoverage

4.26 score 1 stars 13 scripts 176 downloads 7 mentions 24 exports 145 dependencies

Last updated 23 days agofrom:92d4d6f7cd. Checks:OK: 4 WARNING: 3. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-winWARNINGOct 31 2024
R-4.5-linuxOKOct 31 2024
R-4.4-winWARNINGOct 31 2024
R-4.4-macOKOct 31 2024
R-4.3-winWARNINGOct 31 2024
R-4.3-macOKOct 31 2024

Exports:addShadowTextannotateExpressionannotateModificationconvertGeneIdsextractExpressionextractGOseqextractModificationextractModSummaryextractModulesextractScoreshighScoresmakePvalueAnnotationmakePvalueObjectnormalizePvalplotCompareScoresplotDensityPvalplotModuleremoveModificationrunBioNetrunGOseqrunSpinglassscorePvalsearchGOseqstoufferTest

Dependencies:abindAnnotationDbiaskpassbackportsbase64encBHBiasedUrnBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBioNetBiostringsbitbit64bitopsblobbslibcachemcheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydigestdplyrevaluatefansifarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgeneLenDataBasegenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2glueGO.dbgoseqgraphgridExtragtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2igraphIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslorg.Hs.eg.dbpillarpkgconfigplogrplyrpngprettyunitsprogresspurrrR6rappdirsRBGLRColorBrewerRcppRCurlreactome.dbrestfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextxdbmakerUCSC.utilsutf8vctrsviridisviridisLitewithrxfunXMLxml2XVectoryamlzlibbioc

SMITE Vignette

Andrew D. Johnston, N. Ari Wijetunga, and John M. Greally

Rendered fromSMITE.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2020-01-30
Started: 2016-02-12

Readme and manuals

Help Manual

Help pageTopics
Significance-based Modules Integrating the Transcriptome and EpigenomeSMITE-package SMITE
Add shadow text (a second color bordering the text) to a plotaddShadowText addShadowText,ANY-method
Adding expression data to a PvalueAnnotationannotateExpression annotateExpression,PvalueAnnotation-method
Adding modification data to a PvalueAnnotationannotateModification annotateModification,PvalueAnnotation-method
Convert between gene idsconvertGeneIds convertGeneIds,character,character,character-method
A toy dataset ofcurated RNA-seq to test within SMITEcurated_expressiondata expression_curated
View the expression data stored in a PvalueAnnotationextractExpression extractExpression,PvalueAnnotation-method
View the GOseq pathway analysis after having run Goseq, or search for a term.extractGOseq extractGOseq,PvalueAnnotation-method searchGOseq searchGOseq,PvalueAnnotation-method
Extract some or all loaded modifications or a the summary of combined effectsextractModification extractModification,PvalueAnnotation-method extractModSummary extractModSummary,PvalueAnnotation-method
View specific modules within a PvalueAnnotationextractModules extractModules,PvalueAnnotation-method
Extract scores for all genesextractScores extractScores,PvalueAnnotation-method
A small set of RefSeq genes for convertinggenes genes_for_conversiontest
A bed file annotating Refseq genes for the hg19 genome buildhg19_genes hg19_genes_bed
Generate a vector of the highest scoring geneshighScores highScores,PvalueAnnotation-method
A toy dataset of H3k4me1 peaks to test within SMITEh3k4me1 histone_h3k4me1
Initialize a PvalueAnnotationmakePvalueAnnotation makePvalueAnnotation,ANY-method
Function to make a PvalueObject within a PvalueAnnotationmakePvalueObject makePvalueObject,PvalueAnnotation-method
A toy dataset of DNA methylation to test within SMITEmethylation methylationdata
This function normalizes p-values (Scores) that are otherwise on different scales.normalizePval normalizePval,PvalueAnnotation-method
Compare two genomic features by score and display them in a hexbin plotplotCompareScores plotCompareScores,PvalueAnnotation-method
Plot the density of the combined scores stored in a PvalueObjectplotDensityPval plotDensityPval,PvalueAnnotation-method
Plot a specific module after running Spinglass algorithmplotModule plotModule,PvalueAnnotation-method
An Igraph network for REACTOME with nodes as gene symbolsREACTOME Reactome.Symbol.Igraph
A function to "unload" a modification that has already been added.removeModification removeModification,PvalueAnnotation-method
Perform BioNet Analysis on a PvalueAnnotationrunBioNet runBioNet,PvalueAnnotation-method
Run a GoSeq pathway analysisrunGOseq runGOseq,PvalueAnnotation-method
Run Spinglass algorithm on a Scored PvalueAnnotationrunSpinglass runSpinglass,PvalueAnnotation-method
Making a single combined score for each genescorePval scorePval,PvalueAnnotation-method
Stouffer's TeststoufferTest stoufferTest,vector-method
A toy PvalueAnnotationtest_annotation test_annotation_score_data