Package: sesameData 1.30.0

Wanding Zhou

sesameData: Supporting Data for SeSAMe Package

Provides supporting annotation and test data for SeSAMe package. This includes chip tango addresses, mapping information, performance annotation, and trained predictor for Infinium array data. This package provides user access to essential annotation data for working with many generations of the Infinium DNA methylation array. Currently we support human array (HM27, HM450, EPIC), mouse array (MM285) and the HorvathMethylChip40 (Mammal40) array.

Authors:Wanding Zhou [aut, cre, fnd], Hui Shen [aut, fnd], Timothy Triche [ctb]

sesameData_1.30.0.tar.gz
sesameData_1.30.0.tar.gz(r-4.7-any)sesameData_1.30.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
sesameData/json (API)

# Install 'sesameData' in R:

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

Bug tracker:https://github.com/zwdzwd/sesame/issues

On BioConductor:sesameData-1.31.0(data/experiment 3.24)sesameData-1.30.0(data/experiment 3.23)

experimentdata microarraydata genome experimenthub methylationarraydata bioinformatics dna-methylation microarray datapkg

9.92 score 84 stars 4 packages 158 scripts 16 exports 65 dependencies

Last updated from:5e962cdab7 (on RELEASE_3_23). Checks:1 NOTE, 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	NOTE	167
linux-devel	OK	354
source / vignettes	OK	564
linux-release	OK	327

Exports:inferPlatformFromProbeIDs sesameData_annoProbes sesameData_check_genome sesameData_check_platform sesameData_getGenomeInfo sesameData_getManifestGRanges sesameData_getProbesByGene sesameData_getProbesByRegion sesameData_getTxnGRanges sesameData_txnToGeneGRanges sesameDataCache sesameDataCacheAll sesameDataGet sesameDataGet_resetEnv sesameDataHas sesameDataList

Dependencies:AnnotationDbi AnnotationHub askpass Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocManager BiocVersion Biostrings bit bit64 blob cachem cli clipr cpp11 crayon curl DBI dbplyr dplyr ExperimentHub fastmap filelock generics GenomicRanges glue hms httr httr2 IRanges jsonlite KEGGREST lifecycle magrittr memoise mime openssl pillar pkgconfig png prettyunits progress purrr R6 rappdirs readr rlang RSQLite S4Vectors Seqinfo stringi stringr sys tibble tidyr tidyselect tzdb utf8 vctrs vroom withr XVector yaml

SeSAMe Data User Guide

Rendered fromsesameData.Rmdusingknitr::rmarkdown

Last update: 2026-01-07
Started: 2018-05-29

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
build GENCODE gtf	build_GENCODE_gtf
Master data frame for all object to cache	df_master
Extend a GRanges	extend
infer platform from Probe_IDs	inferPlatformFromProbeIDs
Annotate Probes by Probe ID	sesameData_annoProbes
Find genome assembly version(s) supported for a platform	sesameData_check_genome
Check platform code	sesameData_check_platform
Get genome info files	sesameData_getGenomeInfo
get Infinium manifest GRanges	sesameData_getManifestGRanges
Get Probes by Genes or Gene Promoters	sesameData_getProbesByGene
Get probes by genomic region	sesameData_getProbesByRegion
convert GRangesList to transcript GRanges	sesameData_getTxnGRanges
convert transcript GRanges to gene GRanges	sesameData_txnToGeneGRanges
Cache SeSAMe data	sesameDataCache
Cache all SeSAMe data	sesameDataCacheAll
Get SeSAMe data	sesameDataGet
Check whether the title exists in cacheEnv	sesameDataGet_checkEnv
Empty cache environment to free memory	sesameDataGet_resetEnv
Whether sesameData has	sesameDataHas
List all SeSAMe data	sesameDataList