Package: mCSEA 1.33.0

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_1.33.0.tar.gz
mCSEA_1.33.0.zip(r-4.7)mCSEA_1.33.0.zip(r-4.6)mCSEA_1.33.0.zip(r-4.5)
mCSEA_1.33.0.tgz(r-4.6-any)mCSEA_1.33.0.tgz(r-4.5-any)
mCSEA_1.33.0.tar.gz(r-4.7-any)mCSEA_1.33.0.tar.gz(r-4.6-any)
mCSEA_1.33.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
mCSEA/json (API)

# 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-1.33.0(bioc 3.24)mCSEA-1.32.0(bioc 3.23)

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

4.60 score 20 scripts 452 downloads 4 mentions 5 exports 157 dependencies

Last updated from:283bcc89f1. Checks:8 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	610
linux-devel-x86_64	ERROR	832
source / vignettes	OK	809
linux-release-x86_64	ERROR	839
macos-release-arm64	ERROR	498
macos-oldrel-arm64	ERROR	502
windows-devel	ERROR	690
windows-release	ERROR	742
windows-oldrel	ERROR	700
wasm-release	OK	541

Exports:mCSEAIntegrate mCSEAPlot mCSEAPlotGSEA mCSEATest rankProbes

Dependencies:abind AnnotationDbi AnnotationFilter askpass backports base64enc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem checkmate cigarillo cli cluster codetools colorspace cowplot cpp11 crayon curl data.table DBI dbplyr DelayedArray deldir dichromat digest dplyr ensembldb evaluate farver fastmap fastmatch fgsea filelock fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb 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 mime nnet openssl org.Hs.eg.db OrganismDbi pillar pkgconfig png prettyunits progress ProtGenerics purrr R6 rappdirs RBGL RColorBrewer Rcpp RcppEigen RCurl restfulr Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors S7 sass scales Seqinfo snow SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex TxDb.Hsapiens.UCSC.hg19.knownGene UCSC.utils utf8 VariantAnnotation vctrs viridisLite withr xfun XML xml2 XVector yaml

DMRs identification with mCSEA package

Rendered frommCSEA.Rmdusingknitr::rmarkdown

Last update: 2020-02-18
Started: 2017-11-16

Citation

Development and contributors

Readme and manuals

Help Manual

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