Package: methylGSA 1.25.0

Xu Ren

methylGSA: Gene Set Analysis Using the Outcome of Differential Methylation

The main functions for methylGSA are methylglm and methylRRA. methylGSA implements logistic regression adjusting number of probes as a covariate. methylRRA adjusts multiple p-values of each gene by Robust Rank Aggregation. For more detailed help information, please see the vignette.

Authors:Xu Ren [aut, cre], Pei Fen Kuan [aut]

methylGSA_1.25.0.tar.gz
methylGSA_1.25.0.zip(r-4.5)methylGSA_1.25.0.zip(r-4.4)
methylGSA_1.25.0.tgz(r-4.4-any)methylGSA_1.23.0.tgz(r-4.3-any)
methylGSA_1.25.0.tar.gz(r-4.5-noble)methylGSA_1.25.0.tar.gz(r-4.4-noble)
methylGSA_1.25.0.tgz(r-4.4-emscripten)methylGSA_1.25.0.tgz(r-4.3-emscripten)
methylGSA.pdf |methylGSA.html✨
methylGSA/json (API)
NEWS

# Install 'methylGSA' in R:

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

Bug tracker:https://github.com/reese3928/methylgsa/issues

Datasets:

CpG2Gene - An example of user user-supplied mapping between CpGs and genes
GS.list - An example of user input gene sets
cpg.pval - An example of user input cpg.pval

On BioConductor:methylGSA-1.23.0(bioc 3.20)methylGSA-1.22.0(bioc 3.19)

dnamethylation differentialmethylation genesetenrichment regression generegulation pathways enrichment generalized-linear-models logistic-regression methylation ontology shiny

6.90 score 11 stars 36 scripts 276 downloads 11 mentions 8 exports 206 dependencies

Last updated 2 months agofrom:fb33fc35d7. Checks:OK: 1 NOTE: 5. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	NOTE	Oct 31 2024
R-4.5-linux	NOTE	Oct 30 2024
R-4.4-win	NOTE	Oct 31 2024
R-4.4-mac	NOTE	Oct 31 2024
R-4.3-mac	NOTE	Oct 10 2024

Exports:barplot getDescription getGS methylglm methylgometh methylRRA prepareAnnot runExample

Dependencies:abind annotate AnnotationDbi ape aplot askpass base64 base64enc beanplot BH BiasedUrn Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob bslib bumphunter cachem cli clipr clusterProfiler codetools colorspace commonmark cowplot cpp11 crayon curl data.table DBI DelayedArray DelayedMatrixStats digest doRNG DOSE dplyr enrichplot fansi farver fastmap fastmatch FDb.InfiniumMethylation.hg19 fgsea fontawesome foreach formatR fs futile.logger futile.options genefilter generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges GEOquery ggforce ggfun ggnewscale ggplot2 ggplotify ggrepel ggtangle ggtree glue GO.db GOSemSim gridExtra gridGraphics gson gtable HDF5Array hms htmltools httpuv httr httr2 igraph IlluminaHumanMethylation450kanno.ilmn12.hg19 IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno.ilm10b4.hg19 IlluminaHumanMethylationEPICmanifest IlluminaHumanMethylationEPICv2anno.20a1.hg38 IlluminaHumanMethylationEPICv2manifest illuminaio IRanges isoband iterators jquerylib jsonlite KEGGREST labeling lambda.r later lattice lazyeval lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats mclust memoise methylumi mgcv mime minfi missMethyl multtest munsell nlme nor1mix openssl org.Hs.eg.db patchwork pillar pkgconfig plogr plyr png polyclip preprocessCore prettyunits progress promises purrr quadprog qvalue R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl reactome.db readr rentrez reshape reshape2 restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rngtools RobustRankAggreg Rsamtools RSQLite rtracklayer ruv rvest S4Arrays S4Vectors sass scales scatterpie scrime selectr shiny siggenes snow sourcetools SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment survival sys systemfonts tibble tidyr tidyselect tidytree treeio tweenr TxDb.Hsapiens.UCSC.hg19.knownGene tzdb UCSC.utils utf8 vctrs viridisLite vroom withr XML xml2 xtable XVector yaml yulab.utils zlibbioc

methylGSA: Gene Set Analysis for DNA Methylation Datasets

Xu Ren and Pei Fen Kuan

Rendered frommethylGSA-vignette.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2021-05-08
Started: 2018-06-06

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Barplot for methylGSA analysis result	barplot
An example of user input cpg.pval	cpg.pval
An example of user user-supplied mapping between CpGs and genes	CpG2Gene
Get CpG annotation	getAnnot
Get gene set description	getDescription
Get Gene Sets	getGS
An example of user input gene sets	GS.list
Implement logistic regression adjusting for number of probes in enrichment analysis	methylglm
Adjusting number of probes in gene set testing using gometh or gsameth in missMethyl	methylgometh
Enrichment analysis after adjusting multiple p-values of each gene by Robust Rank Aggregation	methylRRA
Prepare user-supplied mapping between CpGs and genes.	prepareAnnot
methylGSA shiny app	runExample