Package: RITAN 1.37.0

Michael Zimmermann

RITAN: Rapid Integration of Term Annotation and Network resources

Tools for comprehensive gene set enrichment and extraction of multi-resource high confidence subnetworks. RITAN facilitates bioinformatic tasks for enabling network biology research.

Authors:Michael Zimmermann [aut, cre]

RITAN_1.37.0.tar.gz
RITAN_1.37.0.zip(r-4.7)RITAN_1.37.0.zip(r-4.6)RITAN_1.37.0.zip(r-4.5)
RITAN_1.37.0.tgz(r-4.6-any)RITAN_1.37.0.tgz(r-4.5-any)
RITAN_1.37.0.tar.gz(r-4.7-any)RITAN_1.37.0.tar.gz(r-4.6-any)
RITAN_1.37.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RITAN/json (API)

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

On BioConductor:RITAN-1.37.0(bioc 3.24)RITAN-1.36.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

qualitycontrolnetworknetworkenrichmentnetworkinferencegenesetenrichmentfunctionalgenomicsgraphandnetwork

5.72 score 14 scripts 5 mentions 16 exports 147 dependencies

Last updated from:f3a935df74. Checks:8 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING305
linux-devel-x86_64WARNING533
source / vignettesOK483
linux-release-x86_64WARNING541
macos-release-arm64WARNING295
macos-oldrel-arm64WARNING227
windows-develWARNING344
windows-releaseWARNING357
windows-oldrelWARNING372
wasm-releaseOK285

Exports:as.graphcheck_any_net_inputcheck_net_inputenrichment_symbolsgeneset_overlapicon_testload_geneset_symbolsnetwork_overlapreadGMTreadSIFresource_reduceshow_active_genesets_histterm_enrichmentterm_enrichment_by_subsetwrite_simple_tablewriteGMT

Dependencies:abindanndataAnnotationDbiAnnotationFilteraskpassassertthatbasiliskBgeeDBBHBiobaseBiocBaseUtilsBiocGenericsBiocIObiocmakeBiocParallelBiostringsbitbit64bitopsblobbreadcachemcaToolschroncigarilloclicodetoolscpp11crayoncurldata.tableDBIDelayedArraydigestdir.expirydplyrdynamicTreeCutEnsDb.Hsapiens.v86ensembldbevaluateexpmfarverfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2glueGO.dbgplotsgraphgridExtragsubfngtablegtoolsh5mreadhashHDF5ArrayherehighrhttrigraphIRangesisobandjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlatticelazyevallifecyclemagrittrMatrixMatrixGenericsmatrixStatsMCLmemoisemimeopensslpillarpkgconfigplotrixplyrpngProtGenericsprotopurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppTOMLRCurlreshape2restfulrreticulaterhdf5rhdf5filtersRhdf5libRhtslibRITANdatarjsonrlangrprojrootRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7scalesSeqinfoSingleCellExperimentsnowSparseArraySparseMsqldfSTRINGdbstringistringrSummarizedExperimentsystibbletidyrtidyselecttopGOUCSC.utilsutf8vctrsviridisLitewithrxfunXMLXVectoryamlzellkonverter

Enrichment Vignette
Introduction to RITAN | Quick Start | Full Example of Enrichment Analysis in RITAN | Add an Annotation Matrix | Show the Number of Genes | Term Enrichment | Term Enrichment Using Other Resources | Term Enrichment for User-Input Resource | Term Enrichment for User-Defined Terms | References
Rendered fromenrichment.Rmdusingknitr::rmarkdown

Last update: 2020-02-18
Started: 2017-03-03

Multi-Tissue Analysis
Enrichment to Identify Tissue-Specific Patterns
Rendered frommulti_tissue_analysis.Rmdusingknitr::rmarkdown

Last update: 2018-08-30
Started: 2017-09-20

Network Biology (Induced Subnetwork) Vignette
Rendered fromsubnetworks.Rmdusingknitr::rmarkdown

Last update: 2018-08-13
Started: 2017-03-03

Choosing Resources
Resources Indexed by default | Example: Protein Complexes & Protein-Protein Interaction (PPI) | Example: Metabolic Network Interaction | Example: Expression Signalling
Rendered fromchoosing_resources.Rmdusingknitr::rmarkdown

Last update: 2018-08-07
Started: 2017-09-20

Relationships Among Resources
Identify relationships between genesets
Rendered fromresource_relationships.Rmdusingknitr::rmarkdown

Last update: 2018-03-09
Started: 2017-09-20