Package: TENET.ExperimentHub 1.4.0

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_1.4.0.tar.gz
TENET.ExperimentHub_1.4.0.tar.gz(r-4.7-any)TENET.ExperimentHub_1.4.0.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-release.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)

experimenthub experimentdata homo_sapiens_data cancerdata breastcancerdata microarraydata expressiondata rnaseqdata methylationarraydata genome cellculture tissue datapkg

5.18 score 1 packages 4 scripts 6 exports 77 dependencies

Last updated from:5dca57130f (on RELEASE_3_23). Checks:3 NOTE, 1 OK. Indexed: no.

This is a data package. Data packages may be large and do not get checked across all platforms.

Target	Result	Time
bioc-checks	NOTE	258
linux-devel	NOTE	428
source / vignettes	OK	627
linux-release	NOTE	432

Exports:exampleTENETClinicalDataFrame exampleTENETMultiAssayExperiment exampleTENETPeakRegions exampleTENETStep1MakeExternalDatasetsGRanges exampleTENETStep2GetDifferentiallyMethylatedSitesPuritySummarizedExperiment exampleTENETTADRegions

Dependencies:abind AnnotationDbi AnnotationHub askpass Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocManager BiocVersion Biostrings bit bit64 blob cachem cli cpp11 crayon curl DBI dbplyr DelayedArray dplyr ExperimentHub farver fastmap filelock generics GenomicRanges ggplot2 glue gtable httr httr2 IRanges isoband jsonlite KEGGREST labeling lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime MultiAssayExperiment openssl pillar pkgconfig png purrr R6 rappdirs RColorBrewer rlang RSQLite S4Arrays S4Vectors S7 scales Seqinfo SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect utf8 vctrs viridisLite withr XVector yaml

Using the TENET.ExperimentHub datasets

Rendered fromTENET.ExperimentHub_vignette.Rmdusingknitr::rmarkdown

Last update: 2025-10-26
Started: 2024-10-15

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Example TENET clinical data frame	exampleTENETClinicalDataFrame
Example TENET MultiAssayExperiment object	exampleTENETMultiAssayExperiment
Example TENET peak regions	exampleTENETPeakRegions
Example TENET 'step1MakeExternalDatasets' GRanges object	exampleTENETStep1MakeExternalDatasetsGRanges
Example TENET 'step2GetDifferentiallyMethylatedSites' purity SummarizedExperiment object	exampleTENETStep2GetDifferentiallyMethylatedSitesPuritySummarizedExperiment
Example TENET topologically associating domain (TAD) regions	exampleTENETTADRegions