Package: TumourMethData 1.11.0

Richard Heery

TumourMethData: A Collection of DNA Methylation Datasets for Human Tumour Samples and Matching Normal Samples

TumourMethData collects tumour methylation data from a variety of different tumour types (and also matching normal samples where available) and produced with different technologies (e.g. WGBS, RRBS and methylation arrays) and provides them as RangedSummarizedExperiments. This facilitates easy extraction of methylation data for regions of interest across different tumour types and studies.

Authors:Richard Heery [aut, cre]

TumourMethData_1.11.0.tar.gz
TumourMethData_1.11.0.tar.gz(r-4.7-any)TumourMethData_1.11.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
TumourMethData/json (API)

# Install 'TumourMethData' in R:

install.packages('TumourMethData', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/richardheery/tumourmethdata/issues

Uses libs:

openjdk– OpenJDK Java runtime, using Hotspot JIT

Datasets:

TumourMethDatasets - TumourMethDatasets

On BioConductor:TumourMethData-1.11.0(data/experiment 3.24)TumourMethData-1.9.0(data/experiment 3.23)

experimentdata experimenthub methylseqdata cancerdata homo_sapiens_data datapkg openjdk

3.90 score 8 scripts 2 exports 221 dependencies

Last updated from:46455f70ce. Checks:1 WARNING, 2 NOTE, 1 OK. Indexed: yes.

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

Target	Result	Time
bioc-checks	WARNING	220
linux-devel	NOTE	2333
source / vignettes	OK	2285
linux-release	NOTE	1545

Exports:download_meth_dataset download_rnaseq_dataset

Dependencies:abind AnnotationDbi AnnotationForge AnnotationHub AnnotationHubData askpass assorthead base64enc beachmat BH Biobase BiocBaseUtils BiocCheck BiocFileCache BiocGenerics BiocIO biocmake BiocManager BiocParallel BiocStyle BiocVersion biocViews Biostrings bit bit64 bitops blob bookdown brew brio BSgenome BSgenome.Hsapiens.UCSC.hg19 bslib bsseq cachem callr cigarillo cli clipr codetools commonmark cowplot cpp11 crayon credentials curl data.table DBI dbplyr DelayedArray DelayedMatrixStats desc devtools diffobj digest dir.expiry downlit dplyr ellipsis evaluate ExperimentHub ExperimentHubData fansi farver fastmap filelock fontawesome foreach formatR fs futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicDataCommons GenomicFeatures GenomicRanges gert ggplot2 gitcreds glue graph gtable gtools h5mread HDF5Array highr hms htmltools htmlwidgets httpuv httr httr2 ini IRanges isoband iterators jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice lifecycle limma locfit magrittr Matrix MatrixGenerics matrixStats memoise methodical methrix mime miniUI MultiAssayExperiment openssl openxlsx OrganismDbi otel pak permute pillar pkgbuild pkgconfig pkgdown pkgload png praise prettyunits processx profvis progress promises ps purrr R.methodsS3 R.oo R.utils R6 ragg RaggedExperiment rappdirs RBGL rcmdcheck RColorBrewer Rcpp RcppRoll RCurl rdtools readr remotes restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rJava rjson rlang rmarkdown roxygen2 rprojroot Rsamtools RSQLite rstudioapi rtracklayer RUnit rversions rvest S4Arrays S4Vectors S7 sass scales selectr Seqinfo sessioninfo shiny snow sourcetools SparseArray sparseMatrixStats statmod stringdist stringi stringr SummarizedExperiment sys systemfonts TCGAutils testthat textshaping tibble tidyr tidyselect tinytex tzdb UCSC.utils urlchecker usethis utf8 vctrs viridisLite vroom waldo whisker withr xfun xlsx xlsxjars XML xml2 xopen xtable XVector yaml zip

Getting Tumour Methylation Data with TumourMethData

Introduction | Downloading data | SessionInfo

Rendered fromgetting_tumour_methylation_from_TumourMethData.Rmdusingknitr::rmarkdown

Last update: 2023-10-16
Started: 2023-09-29

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
TumourMethData: A collection of DNA methylation datasets for human tumour samples and matching normal samples	TumourMethData-package TumourMethData
Download a WGBS methylation dataset from TumourMethData	download_meth_dataset
Download a RNA-Seq counts dataset from TumourMethData	download_rnaseq_dataset
TumourMethDatasets	TumourMethDatasets