Package: DExMA 1.13.0

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_1.13.0.tar.gz
DExMA_1.13.0.zip(r-4.5)DExMA_1.13.0.zip(r-4.4)DExMA_1.13.0.zip(r-4.3)
DExMA_1.13.0.tgz(r-4.4-any)DExMA_1.13.0.tgz(r-4.3-any)
DExMA_1.13.0.tar.gz(r-4.5-noble)DExMA_1.13.0.tar.gz(r-4.4-noble)
DExMA_1.13.0.tgz(r-4.4-emscripten)DExMA_1.13.0.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.

bioconductor-package

12 exports 0.91 score 112 dependencies

Last updated 2 months agofrom:5d23315c8c

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

Dependencies: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 DExMAdata dplyr edgeR fansi farver fastmap formatR futile.logger futile.options genefilter generics GenomeInfoDb GenomeInfoDbData GEOquery glue gplots gtable gtools hms httr 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 RColorBrewer Rcpp readr rlang RSQLite S4Vectors scales snow snpStats statmod stringi stringr 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 Jun 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