Package: miRspongeR 2.16.0
Junpeng Zhang
miRspongeR: Identification and analysis of miRNA sponge regulation
This package provides several functions to explore miRNA sponge (also called ceRNA or miRNA decoy) regulation from putative miRNA-target interactions or/and transcriptomics data (including bulk, single-cell and spatial gene expression data). It provides eight popular methods for identifying miRNA sponge interactions, and an integrative method to integrate miRNA sponge interactions from different methods, as well as the functions to validate miRNA sponge interactions, and infer miRNA sponge modules, conduct enrichment analysis of miRNA sponge modules, and conduct survival analysis of miRNA sponge modules. By using a sample control variable strategy, it provides a function to infer sample-specific miRNA sponge interactions. In terms of sample-specific miRNA sponge interactions, it implements three similarity methods to construct sample-sample correlation network.
Authors:
miRspongeR_2.16.0.tar.gz
miRspongeR_2.16.0.zip(r-4.7)miRspongeR_2.16.0.zip(r-4.6)miRspongeR_2.16.0.zip(r-4.5)
miRspongeR_2.16.0.tgz(r-4.6-x86_64)miRspongeR_2.16.0.tgz(r-4.6-arm64)miRspongeR_2.16.0.tgz(r-4.5-x86_64)miRspongeR_2.16.0.tgz(r-4.5-arm64)
miRspongeR_2.16.0.tar.gz(r-4.7-arm64)miRspongeR_2.16.0.tar.gz(r-4.7-x86_64)miRspongeR_2.16.0.tar.gz(r-4.6-arm64)miRspongeR_2.16.0.tar.gz(r-4.6-x86_64)
miRspongeR_2.16.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
miRspongeR/json (API)
NEWS
| # Install 'miRspongeR' in R: |
| install.packages('miRspongeR', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/zhangjunpeng411/mirsponger/issues
On BioConductor:miRspongeR-2.17.0(bioc 3.24)miRspongeR-2.16.0(bioc 3.23)
geneexpressionbiomedicalinformaticsnetworkenrichmentsurvivalmicroarraysoftwaresinglecellspatialrnaseqcernamirnaspongecpp
Last updated from:740d8fdc31 (on RELEASE_3_23). Checks:1 WARNING, 11 NOTE, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 364 | ||
| linux-devel-arm64 | NOTE | 519 | ||
| linux-devel-x86_64 | NOTE | 544 | ||
| source / vignettes | OK | 560 | ||
| linux-release-arm64 | NOTE | 462 | ||
| linux-release-x86_64 | NOTE | 518 | ||
| macos-release-arm64 | NOTE | 413 | ||
| macos-release-x86_64 | NOTE | 694 | ||
| macos-oldrel-arm64 | NOTE | 366 | ||
| macos-oldrel-x86_64 | NOTE | 853 | ||
| windows-devel | NOTE | 837 | ||
| windows-release | NOTE | 902 | ||
| windows-oldrel | NOTE | 798 | ||
| wasm-release | OK | 311 |
Exports:integrateMethodmoduleDEAmoduleFEAmoduleSurvivalnetModulequerymiRTargetbindingsample_cor_networksponge_sample_specificspongeMethodspongeValidate
Dependencies:abindaisdkAnnotationDbiapeaplotaskpassbackportsbase64encbayestestRBiobaseBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64blobbootbroombslibcachemcallrcarcarDatacaretcellrangercheckmatecirclizeclassclicliprclockclueclusterclusterProfilercodetoolscolorspaceComplexHeatmapconflictedcorpcorcorrplotcowplotcpp11crayoncurlcvmsdata.tabledatawizardDBIdbplyrDerivdiagramdigestdir.expirydoBydoParalleldoRNGDOSEdplyrdtplyre1071enrichitenrichplotevaluateexpmfarverfastmapfilelockfontawesomefontBitstreamVerafontLiberationfontquiverforcatsforeachforecastFormulafracdifffsfuturefuture.applygarglegdtoolsgenericsGetoptLongggforceggfunggiraphggnewscaleggplot2ggplotifyggpubrggraphggrepelggridgesggsciggsignifggtangleggtreeglmnetGlobalOptionsglobalsglueGO.dbgoogledrivegooglesheets4GOSemSimgowergraphgraphitegraphlayoutsgRbasegridExtragridGraphicsgroupdata2gsongtablehardhathavenhighrhmshtmltoolshtmlwidgetshttrhttr2idsigraphinsightipredIRangesisobanditeratorsjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglatticelavalazyevallifecyclelistenvlme4lmtestlogginglubridatemagrittrMASSMatrixMatrixModelsmatrixStatsMCLmemoiseMetBrewermgcvmicrobenchmarkmimeminqaModelMetricsmodelrMuMInnlmenloptrnnetnumbersnumDerivopensslorg.Hs.eg.dbparallellyparameterspatchworkpbkrtestpillarpkgconfigplyrpngpolyclippolynomppcorprettyunitspROCprocessxprodlimprogressprogressrproxypspurrrquantregqvalueR6raggrandomForestrappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreactome.dbReactomePAreadrreadxlrearrrrecipesreformulasrematchrematch2reprexreshape2rjsonrlangrmarkdownrngtoolsrpartRSQLiterstatixrstudioapirvestS4VectorsS7sassscalesscatterpieselectrSeqinfoshapeSparseMsparsevctrsSPONGESQUAREMstringistringrsurvivalsyssystemfontstextshapingtibbletidydrtidygraphtidyrtidyselecttidytreetidyversetimechangetimeDatetinytextnettreeiotweenrtzdburcautf8uuidvctrsviridisviridisLitevroomwithrxfunxml2XVectoryamlyulab.utilszoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Integrate method for identifying miRNA sponge interactions by integrating different methods | integrateMethod |
| Disease enrichment analysis of modules | moduleDEA |
| Functional GO, KEGG and Reactome enrichment analysis of modules | moduleFEA |
| Survival analysis of modules | moduleSurvival |
| Identifying miRNA sponge modules from network | netModule |
| A null model for testing purposes in SPONGE R package | precomputed_null_model |
| Query miRNA-target interactions by combining expression data and putative miRNA-target interactions | querymiRTargetbinding |
| Identifying sample-sample correlation network | sample_cor_network |
| Identifying sample-specific miRNA sponge interactions | sponge_sample_specific |
| Identifying miRNA sponge interactions | spongeMethod |
| Validation of computationally predicted miRNA sponge interactions | spongeValidate |