Package: DMRcatedata 2.30.0

Tim Peters

DMRcatedata: Data Package for DMRcate

This package contains 9 data objects supporting functionality and examples of the Bioconductor package DMRcate.

Authors:Tim Peters

DMRcatedata_2.30.0.tar.gz
DMRcatedata_2.30.0.tar.gz(r-4.7-any)DMRcatedata_2.30.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
DMRcatedata/json (API)

# Install 'DMRcatedata' in R:

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

On BioConductor:DMRcatedata-2.31.0(data/experiment 3.24)DMRcatedata-2.30.0(data/experiment 3.23)

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

experimenthub experimentdata snpdata homo_sapiens_data mus_musculus_data sequencingdata microarraydata genome datapkg

3.38 score 12 scripts 0 exports 198 dependencies

Last updated from:f69006f7c8 (on RELEASE_3_23). Checks:1 ERROR, 3 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	ERROR	397
linux-devel	OK	544
source / vignettes	OK	541
linux-release	OK	551

Exports:

Dependencies:abind annotate AnnotationDbi AnnotationFilter AnnotationHub askpass backports base64 base64enc beanplot BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO biocmake BiocManager BiocParallel BiocVersion biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bslib bumphunter cachem cellranger checkmate cigarillo cli clipr cluster codetools colorspace cpp11 crayon curl data.table DBI dbplyr DelayedArray DelayedMatrixStats deldir dichromat digest dir.expiry doRNG dplyr ensembldb evaluate ExperimentHub farver fastmap filelock fontawesome foreach foreign formatR Formula fs futile.logger futile.options genefilter generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GEOquery ggplot2 glue gridExtra gtable Gviz h5mread HDF5Array highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 IlluminaHumanMethylation450kanno.ilmn12.hg19 IlluminaHumanMethylationEPICanno.ilm10b4.hg19 illuminaio interp IRanges isoband iterators jpeg jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice latticeExtra lazyeval lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats mclust memoise mime minfi multtest nlme nnet nor1mix openssl pillar pkgconfig plyr png preprocessCore prettyunits progress ProtGenerics purrr quadprog R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl readr readxl rematch rentrez reshape restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown rngtools rpart Rsamtools RSQLite rstudioapi rtracklayer rvest S4Arrays S4Vectors S7 sass scales scrime selectr Seqinfo siggenes snow SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect tinytex tzdb UCSC.utils utf8 VariantAnnotation vctrs viridisLite vroom withr xfun XML xml2 xtable XVector yaml

The DMRcate package user's guide

Rendered fromDMRcatedata.Rnwusingknitr::knitr

Last update: 2024-03-08
Started: 2019-09-12

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Dataset to use with the DMRcate pipeline	DMRcatedata-package DMRcatedata
EPICv2 beta values for DMR calling	ALLbetas
Potentially cross-hybridising Illumina probes	crosshyb
SNP information for EPICv2 Illumina probes	epicv2snps
Start and stop positions of all genes in hg19	hg19.generanges
GeneRegionTrack for hg19	hg19.grt
Start and stop positions of all genes in hg38	hg38.generanges
GeneRegionTrack for hg38	hg38.grt
Start and stop positions of all genes in mm10	mm10.generanges
GeneRegionTrack for mm10	mm10.grt
SNP information for EPICv1 and 450K Illumina probes	snpsall
Sex chromosome Illumina probes	XY.probes