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:
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-4.5-any)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-1.15.0(bioc 3.21)DExMA-1.14.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
differentialexpressiongeneexpressionstatisticalmethodqualitycontrol
Last updated 4 months agofrom:655549d660. Checks:7 OK, 1 WARNING. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Feb 14 2025 |
| R-4.5-win | OK | Feb 14 2025 |
| R-4.5-mac | WARNING | Feb 14 2025 |
| R-4.5-linux | OK | Feb 14 2025 |
| R-4.4-win | OK | Feb 14 2025 |
| R-4.4-mac | OK | Feb 14 2025 |
| R-4.3-win | OK | Feb 14 2025 |
| R-4.3-mac | OK | Feb 14 2025 |
Exports:allSameIDbatchRemovecalculateEScreateObjectMAdataLogdownloadGEODataelementObjectMAheterogeneityTestmakeHeatmapmetaAnalysisDEmissGenesImputpvalueIndAnalysis
Dependencies:abindamapannotateAnnotationDbiaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64bitopsblobbnstructcachemcaToolsclicliprcodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArrayDExMAdatadplyredgeRfansifarverfastmapformatRfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGEOquerygluegplotsgtablegtoolshmshttrhttr2igraphimputeIRangesjsonliteKEGGRESTKernSmoothlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpheatmappillarpkgconfigplogrplyrpngprettyunitsprogresspurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppreadrrentrezrlangRSQLitervestS4ArraysS4VectorsscalesselectrsnowsnpStatsSparseArraystatmodstringistringrSummarizedExperimentsurvivalsvaswampsystibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsviridisLitevroomwithrXMLxml2xtableXVectorzlibbioc
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 |
