Package: TENET.ExperimentHub 1.5.0

Rhie Lab at the University of Southern California

TENET.ExperimentHub: Experiment data for the TENET package

ExperimentHub package containing datasets for use in the TENET package's vignette and function examples. These include a variety of different objects to illustrate different datasets used in TENET functions. Where applicable, all datasets are aligned to the hg38 human genome.

Authors:Rhie Lab at the University of Southern California [cre], Daniel Mullen [aut], Zexun Wu [aut], Ethan Nelson-Moore [aut], Suhn Rhie [aut]

TENET.ExperimentHub_1.5.0.tar.gz
TENET.ExperimentHub_1.5.0.tar.gz(r-4.7-any)TENET.ExperimentHub_1.5.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
TENET.ExperimentHub/json (API)

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

Bug tracker:https://github.com/rhielab/tenet.experimenthub/issues

On BioConductor:TENET.ExperimentHub-1.5.0(data/experiment 3.24)TENET.ExperimentHub-1.4.0(data/experiment 3.23)

experimenthubexperimentdatahomo_sapiens_datacancerdatabreastcancerdatamicroarraydataexpressiondatarnaseqdatamethylationarraydatagenomecellculturetissuedatapkg

3.78 score 1 packages 4 scripts 6 exports 78 dependencies

Last updated from:8efd40fe48. Checks:1 ERROR. Indexed: yes.

TargetResultTimeFilesSyslog
source / vignettesERROR-3098

Exports:exampleTENETClinicalDataFrameexampleTENETMultiAssayExperimentexampleTENETPeakRegionsexampleTENETStep1MakeExternalDatasetsGRangesexampleTENETStep2GetDifferentiallyMethylatedSitesPuritySummarizedExperimentexampleTENETTADRegions

Dependencies:abindAnnotationDbiAnnotationHubaskpassBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocManagerBiocVersionBiostringsbitbit64blobcachemclicpp11crayoncurlDBIdbplyrDelayedArraydigestdplyrExperimentHubfarverfastmapfilelockgenericsGenomicRangesggplot2gluegtablehttrhttr2IRangesisobandjsonliteKEGGRESTlabelinglatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeMultiAssayExperimentopensslpillarpkgconfigpngpurrrR6rappdirsRColorBrewerrlangRSQLiteS4ArraysS4VectorsS7scalesSeqinfoSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectutf8vctrsviridisLitewithrXVectoryaml

Readme and manuals

Help Manual

Help pageTopics
Example TENET clinical data frameexampleTENETClinicalDataFrame
Example TENET MultiAssayExperiment objectexampleTENETMultiAssayExperiment
Example TENET peak regionsexampleTENETPeakRegions
Example TENET 'step1MakeExternalDatasets' GRanges objectexampleTENETStep1MakeExternalDatasetsGRanges
Example TENET 'step2GetDifferentiallyMethylatedSites' purity SummarizedExperiment objectexampleTENETStep2GetDifferentiallyMethylatedSitesPuritySummarizedExperiment
Example TENET topologically associating domain (TAD) regionsexampleTENETTADRegions