Package: DExMA 1.15.0

Juan Antonio Villatoro-García

DExMA: Differential Expression Meta-Analysis

performing all the steps of gene expression meta-analysis considering the possible existence of missing genes. It provides the necessary functions to be able to perform the different methods of gene expression meta-analysis. In addition, it contains functions to apply quality controls, download GEO datasets and show graphical representations of the results.

Authors:Juan Antonio Villatoro-García [aut, cre], Pedro Carmona-Sáez [aut]

DExMA_1.15.0.tar.gz
DExMA_1.15.0.zip(r-4.5)DExMA_1.15.0.zip(r-4.4)DExMA_1.15.0.zip(r-4.3)
DExMA_1.15.0.tgz(r-4.4-any)DExMA_1.15.0.tgz(r-4.3-any)
DExMA_1.15.0.tar.gz(r-4.5-noble)DExMA_1.15.0.tar.gz(r-4.4-noble)
DExMA_1.15.0.tgz(r-4.4-emscripten)DExMA_1.15.0.tgz(r-4.3-emscripten)
DExMA.pdf |DExMA.html✨
DExMA/json (API)
NEWS

# Install 'DExMA' in R:

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

On BioConductor:DExMA-1.13.0(bioc 3.20)DExMA-1.12.0(bioc 3.19)

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

differentialexpression geneexpression statisticalmethod qualitycontrol

3.70 score 7 scripts 163 downloads 12 exports 123 dependencies

Last updated 25 days agofrom:655549d660. Checks:OK: 7. Indexed: yes.

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

Exports:allSameID batchRemove calculateES createObjectMA dataLog downloadGEOData elementObjectMA heterogeneityTest makeHeatmap metaAnalysisDE missGenesImput pvalueIndAnalysis

Dependencies:abind amap annotate AnnotationDbi askpass BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 bitops blob bnstruct cachem caTools cli clipr codetools colorspace cpp11 crayon curl data.table DBI DelayedArray DExMAdata dplyr edgeR fansi farver fastmap formatR futile.logger futile.options genefilter generics GenomeInfoDb GenomeInfoDbData GenomicRanges GEOquery glue gplots gtable gtools hms httr httr2 igraph impute IRanges jsonlite KEGGREST KernSmooth labeling lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pheatmap pillar pkgconfig plogr plyr png prettyunits progress purrr R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp readr rentrez rlang RSQLite rvest S4Arrays S4Vectors scales selectr snow snpStats SparseArray statmod stringi stringr SummarizedExperiment survival sva swamp sys tibble tidyr tidyselect tzdb UCSC.utils utf8 vctrs viridisLite vroom withr XML xml2 xtable XVector zlibbioc

Differential Expression Meta-Analysis with DExMA package

Rendered fromDExMA.Rnwusingutils::Sweaveon Oct 30 2024.

Last update: 2023-11-09
Started: 2021-04-08

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Set all datasets in the same ID	allSameID
Elimination of covariates batch effect or bias	batchRemove
Calculation of Effects Sizes and their variance	calculateES
Creation of the object to use in meta-analysis	createObjectMA
Auxiliary function to check if data are log transfromed and transformed if it are not log-transformed	dataLog
Download datasets from GEO database	downloadGEOData
Creation of the object to use in meta-analysis	elementObjectMA
Checking the heterogeneity of the different studies	heterogeneityTest
Visualization of the meta-analysis results	makeHeatmap
Performing Meta-analysis	metaAnalysisDE
Imputation of unmeasured genes	missGenesImput
Calculation p-value for each gene and study	pvalueIndAnalysis