1 Introduction | 2 Previous steps: Meta-analysis object | 3 Performing Meta-analysis | 4 Additional information | 5 Session info
Package: DExMA 1.21.0
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:
DExMA_1.21.0.tar.gz
DExMA_1.21.0.zip(r-4.7)DExMA_1.21.0.zip(r-4.6)DExMA_1.21.0.zip(r-4.5)
DExMA_1.21.0.tgz(r-4.6-any)DExMA_1.21.0.tgz(r-4.5-any)
DExMA_1.21.0.tar.gz(r-4.7-any)DExMA_1.21.0.tar.gz(r-4.6-any)
DExMA_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
DExMA/json (API)
| # Install 'DExMA' in R: |
| install.packages('DExMA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:DExMA-1.21.0(bioc 3.24)DExMA-1.20.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
differentialexpressiongeneexpressionstatisticalmethodqualitycontrol
Last updated from:0653671f0b. Checks:1 WARNING, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 246 | ||
| linux-devel-x86_64 | OK | 406 | ||
| source / vignettes | OK | 362 | ||
| linux-release-x86_64 | OK | 404 | ||
| macos-release-arm64 | OK | 336 | ||
| macos-oldrel-arm64 | OK | 273 | ||
| windows-devel | OK | 315 | ||
| windows-release | OK | 291 | ||
| windows-oldrel | OK | 303 | ||
| wasm-release | OK | 229 |
Exports:allSameIDbatchRemovecalculateEScreateObjectMAdataLogdownloadGEODataelementObjectMAheterogeneityTestmakeHeatmapmetaAnalysisDEmissGenesImputpvalueIndAnalysis
Dependencies:abindamapannotateAnnotationDbiaskpassBHBiobaseBiocFileCacheBiocGenericsBiocParallelBiostringsbitbit64bitopsblobbnstructcachemcaToolsclicliprcodetoolscpp11crayoncurldata.tableDBIdbplyrDelayedArrayDExMAdatadplyredgeRfarverfastmapfilelockformatRfutile.loggerfutile.optionsgenefiltergenericsGenomicRangesGEOquerygluegplotsgtablegtoolshmshttrhttr2igraphimputeIRangesjsonliteKEGGRESTKernSmoothlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimenlmeopensslpheatmappillarpkgconfigplyrpngprettyunitsprogresspurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppreadrrentrezrlangRSQLitervestS4ArraysS4VectorsscalesselectrSeqinfosnowsnpStatsSparseArraystatmodstringistringrSummarizedExperimentsurvivalsvaswampsystibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithrXMLxml2xtableXVector
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 |
