Package: RITAN 1.31.0

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_1.31.0.tar.gz
RITAN_1.31.0.zip(r-4.5)RITAN_1.31.0.zip(r-4.4)RITAN_1.31.0.zip(r-4.3)
RITAN_1.31.0.tgz(r-4.5-any)RITAN_1.31.0.tgz(r-4.4-any)RITAN_1.31.0.tgz(r-4.3-any)
RITAN_1.31.0.tar.gz(r-4.5-noble)RITAN_1.31.0.tar.gz(r-4.4-noble)
RITAN_1.31.0.tgz(r-4.4-emscripten)RITAN_1.31.0.tgz(r-4.3-emscripten)
RITAN.pdf |RITAN.html✨
RITAN/json (API)
NEWS

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

On BioConductor:RITAN-1.31.0(bioc 3.21)RITAN-1.30.0(bioc 3.20)

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

qualitycontrolnetworknetworkenrichmentnetworkinferencegenesetenrichmentfunctionalgenomicsgraphandnetwork

5.40 score 9 scripts 266 downloads 5 mentions 16 exports 152 dependencies

Last updated 4 months agofrom:e6e8dc4b54. Checks:1 OK, 7 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 16 2025
R-4.5-winWARNINGFeb 16 2025
R-4.5-macWARNINGFeb 16 2025
R-4.5-linuxWARNINGFeb 16 2025
R-4.4-winWARNINGFeb 16 2025
R-4.4-macWARNINGFeb 16 2025
R-4.3-winWARNINGFeb 16 2025
R-4.3-macWARNINGFeb 16 2025

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:abindanndataAnnotationDbiAnnotationFilteraskpassassertthatbasiliskbasilisk.utilsBgeeDBBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobbreadcachemcaToolschronclicodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArraydigestdir.expirydplyrdynamicTreeCutEnsDb.Hsapiens.v86ensembldbevaluateexpmfansifarverfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2glueGO.dbgplotsgraphgridExtragsubfngtablegtoolsh5mreadhashHDF5ArrayherehighrhttrigraphIRangesisobandjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlatticelazyevallifecyclelinkcommmagrittrMASSMatrixMatrixGenericsmatrixStatsMCLmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrplotrixplyrpngProtGenericsprotopurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppTOMLRCurlreshape2restfulrreticulaterhdf5rhdf5filtersRhdf5libRhtslibRITANdatarjsonrlangrprojrootRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalesSingleCellExperimentsnowSparseArraySparseMsqldfSTRINGdbstringistringrSummarizedExperimentsystibbletidyrtidyselecttopGOUCSC.utilsutf8vctrsviridisLitewithrxfunXMLXVectoryamlzellkonverter

Choosing Resources

Michael T. Zimmermann

Rendered fromchoosing_resources.Rmdusingknitr::rmarkdownon Feb 16 2025.

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

Enrichment Vignette

Michael T. Zimmermann

Rendered fromenrichment.Rmdusingknitr::rmarkdownon Feb 16 2025.

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

Multi-Tissue Analysis

Michael T. Zimmermann

Rendered frommulti_tissue_analysis.Rmdusingknitr::rmarkdownon Feb 16 2025.

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

Network Biology (Induced Subnetwork) Vignette

Michael T. Zimmermann

Rendered fromsubnetworks.Rmdusingknitr::rmarkdownon Feb 16 2025.

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

Relationships Among Resources

Michael T. Zimmermann

Rendered fromresource_relationships.Rmdusingknitr::rmarkdownon Feb 16 2025.

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