Package: mCSEA 1.27.0

Jordi Martorell-Marugán

mCSEA: Methylated CpGs Set Enrichment Analysis

Identification of diferentially methylated regions (DMRs) in predefined regions (promoters, CpG islands...) from the human genome using Illumina's 450K or EPIC microarray data. Provides methods to rank CpG probes based on linear models and includes plotting functions.

Authors:Jordi Martorell-Marugán and Pedro Carmona-Sáez

mCSEA_1.27.0.tar.gz
mCSEA_1.27.0.zip(r-4.5)mCSEA_1.27.0.zip(r-4.4)mCSEA_1.27.0.zip(r-4.3)
mCSEA_1.27.0.tgz(r-4.4-any)mCSEA_1.27.0.tgz(r-4.3-any)
mCSEA_1.27.0.tar.gz(r-4.5-noble)mCSEA_1.27.0.tar.gz(r-4.4-noble)
mCSEA_1.27.0.tgz(r-4.4-emscripten)mCSEA_1.27.0.tgz(r-4.3-emscripten)
mCSEA.pdf |mCSEA.html✨
mCSEA/json (API)
NEWS

# Install 'mCSEA' in R:

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

Datasets:

exprTest - Expression data example
myRank - Precomputed mCSEA results
myResults - Precomputed mCSEA results

On BioConductor:mCSEA-1.27.0(bioc 3.21)mCSEA-1.25.0(bioc 3.20)

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

immunooncology differentialmethylation dnamethylation epigenetics genetics genomeannotation methylationarray microarray multiplecomparison twochannel

3.08 score 15 scripts 232 downloads 4 mentions 5 exports 162 dependencies

Last updated 23 days agofrom:c8b14765c1. Checks:ERROR: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	FAIL	Oct 31 2024
R-4.5-win	ERROR	Oct 31 2024
R-4.5-linux	ERROR	Oct 31 2024
R-4.4-win	ERROR	Oct 31 2024
R-4.4-mac	ERROR	Oct 31 2024
R-4.3-win	ERROR	Oct 31 2024
R-4.3-mac	ERROR	Oct 31 2024

Exports:mCSEAIntegrate mCSEAPlot mCSEAPlotGSEA mCSEATest rankProbes

Dependencies:abind AnnotationDbi AnnotationFilter askpass backports base64enc BH Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem checkmate cli cluster codetools colorspace cowplot cpp11 crayon curl data.table DBI dbplyr DelayedArray deldir dichromat digest dplyr ensembldb evaluate fansi farver fastmap fastmatch fgsea filelock fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue GO.db graph gridExtra gtable Gviz highr Hmisc hms Homo.sapiens htmlTable htmltools htmlwidgets httr httr2 interp IRanges isoband jpeg jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice latticeExtra lazyeval lifecycle limma magrittr MASS Matrix MatrixGenerics matrixStats mCSEAdata memoise mgcv mime munsell nlme nnet openssl org.Hs.eg.db OrganismDbi pillar pkgconfig plogr png prettyunits progress ProtGenerics purrr R6 rappdirs RBGL RColorBrewer Rcpp RcppEigen RCurl restfulr Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors sass scales snow SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex TxDb.Hsapiens.UCSC.hg19.knownGene txdbmaker UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite withr xfun XML xml2 XVector yaml zlibbioc

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Help page	Topics
Methylated CpGs Set Enrichment Analysis	mCSEA-package mCSEA
Expression data example	exprTest
Integrate methylation and expression	mCSEAIntegrate
Plot mCSEA results	mCSEAPlot
Plot mCSEA results	mCSEAPlotGSEA
mCSEA core analysis	mCSEATest
Precomputed mCSEA results	myRank myResults precomputedmCSEA
Rank CpG probes	rankProbes

Package: mCSEA 1.27.0

mCSEA: Methylated CpGs Set Enrichment Analysis

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Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)