Version Information | Introduction | Package Content | Sample data | Workflow steps | A. Reading Input Data | B. Creating an ExpressionSet Object | C. Principal Variance Component Analysis of the raw data | D. Surrogate Variable Analysis | E. Computing the correlation between the surrogate variables and the covariates | F. Principal Variance Component Analysis of the raw data with the surrogate variables included as covariates | G. Supervised normalization of Microarrays | H. Principal Variance Component Analysis on the normalized data | Discussion | References
Package: ExpressionNormalizationWorkflow 1.39.0
Karthikeyan Murugesan
ExpressionNormalizationWorkflow: Gene Expression Normalization Workflow
An extensive, customized expression normalization workflow incorporating Supervised Normalization of Microarryas(SNM), Surrogate Variable Analysis(SVA) and Principal Variance Component Analysis to identify batch effects and remove them from the expression data to enhance the ability to detect the underlying biological signals.
Authors:
ExpressionNormalizationWorkflow_1.39.0.tar.gz
ExpressionNormalizationWorkflow_1.39.0.zip(r-4.7-any)ExpressionNormalizationWorkflow_1.39.0.zip(r-4.6-any)ExpressionNormalizationWorkflow_1.39.0.zip(r-4.5-any)
ExpressionNormalizationWorkflow_1.39.0.tgz(r-4.6-any)ExpressionNormalizationWorkflow_1.39.0.tgz(r-4.5-any)
ExpressionNormalizationWorkflow_1.39.0.tar.gz(r-4.7-any)ExpressionNormalizationWorkflow_1.39.0.tar.gz(r-4.6-any)
ExpressionNormalizationWorkflow_1.39.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
ExpressionNormalizationWorkflow/json (API)
| # Install 'ExpressionNormalizationWorkflow' in R: |
| install.packages('ExpressionNormalizationWorkflow', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:ExpressionNormalizationWorkflow-1.39.0(workflows 3.24)ExpressionNormalizationWorkflow-1.38.0(workflows 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologyworkflowworkflowgeneexpressionworkflow
Last updated from:1a71bf2886. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 179 | ||
| linux-devel | WARNING | 315 | ||
| source / vignettes | OK | 426 | ||
| linux-release | WARNING | 383 | ||
| macos-release | WARNING | 153 | ||
| macos-oldrel | WARNING | 191 | ||
| windows-devel | WARNING | 200 | ||
| windows-release | WARNING | 199 | ||
| windows-oldrel | WARNING | 195 | ||
| wasm-release | OK | 153 |
Exports:conTocatexpSetobjpvcAnalysnmAnalysurVarAnaly
Dependencies:affyaffyioannotateAnnotationDbiaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocManagerBiocParallelBiostringsbitbit64blobbootcachemclicodetoolscorpcorcpp11crayoncurlDBIedgeRfarverfastmapformatRfutile.loggerfutile.optionsgenefiltergenericsggplot2gluegtablehttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelimmalme4locfitMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminqanlmenloptropensslpkgconfigpngpreprocessCorepvcaR6rbibutilsRColorBrewerRcppRcppEigenRdpackreformulasrlangRSQLiteS4VectorsS7scalesSeqinfosnmsnowstatmodsurvivalsvasysvctrsviridisLitevsnwithrXMLxtableXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Gene Expression Normalization Workflow | ExpressionNormalizationWorkflow |
| Convert continuous values to categorical/discrete values | conTocat |
| Create a compact ExpressionSet Datatype Object | expSetobj |
| Principal variance Component Analysis | pvcAnaly |
| Supervized Normalization of Microarrays | snmAnaly |
| Estimate surrogate covariates unmodeled or hidden in the data | surVarAnaly |