Package: edge 2.39.0

John D. Storey

edge: Extraction of Differential Gene Expression

The edge package implements methods for carrying out differential expression analyses of genome-wide gene expression studies. Significance testing using the optimal discovery procedure and generalized likelihood ratio tests (equivalent to F-tests and t-tests) are implemented for general study designs. Special functions are available to facilitate the analysis of common study designs, including time course experiments. Other packages such as sva and qvalue are integrated in edge to provide a wide range of tools for gene expression analysis.

Authors:John D. Storey, Jeffrey T. Leek and Andrew J. Bass

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NEWS

# Install 'edge' in R:
install.packages('edge', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/jdstorey/edge/issues

Datasets:
  • endotoxin - Gene expression dataset from Calvano et al. (2005) Nature
  • gibson - Gene expression dataset from Idaghdour et al.
  • kidney - Gene expression dataset from Rodwell et al.

On BioConductor:edge-2.39.0(bioc 3.21)edge-2.38.0(bioc 3.20)

multiplecomparisondifferentialexpressiontimecourseregressiongeneexpressiondataimport

7.77 score 21 stars 62 scripts 270 downloads 16 mentions 29 exports 86 dependencies

Last updated 23 days agofrom:b391071f59. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 19 2024
R-4.5-win-x86_64NOTENov 19 2024
R-4.5-linux-x86_64NOTENov 19 2024
R-4.4-win-x86_64NOTENov 19 2024
R-4.4-mac-x86_64NOTENov 19 2024
R-4.4-mac-aarch64NOTENov 19 2024
R-4.3-win-x86_64NOTENov 19 2024
R-4.3-mac-x86_64NOTENov 19 2024
R-4.3-mac-aarch64NOTENov 19 2024

Exports:apply_qvalueapply_svabetaCoefbuild_modelsbuild_studydeSetfit_modelsfitFullfitNullfullMatrixfullMatrix<-fullModelfullModel<-individualindividual<-kl_clustlrtnullMatrixnullMatrix<-nullModelnullModel<-odpqvalueObjqvalueObj<-resFullresNullshowsTypesummary

Dependencies:annotateAnnotationDbiaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobcachemclicodetoolscolorspacecpp11crayoncurlDBIedgeRfansifarverfastmapformatRfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDataggplot2gluegtablehttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrplyrpngqvalueR6RColorBrewerRcppreshape2rlangRSQLiteS4VectorsscalessnowstatmodstringistringrsurvivalsvasystibbleUCSC.utilsutf8vctrsviridisLitewithrXMLxtableXVectorzlibbioc

edge Package

Rendered fromedge.Rnwusingknitr::knitron Nov 19 2024.

Last update: 2024-03-27
Started: 2015-04-14

Readme and manuals

Help Manual

Help pageTopics
Estimate the q-values for a given set of p-valuesapply_qvalue apply_qvalue,deSet-method
Estimate surrogate variablesapply_sva apply_sva,deSet-method
Regression coefficients from full model fitbetaCoef betaCoef,deFit-method
Generate a deSet object with full and null modelsbuild_models
Formulates the experimental modelsbuild_study
The differential expression class for the model fitsdeFit-class
Create a deSet object from an ExpressionSetdeSet deSet,ExpressionSet-method
The differential expression class (deSet)deSet-class
Extraction of Differential Gene Expressionedge-package edge
Gene expression dataset from Calvano et al. (2005) Natureendotoxin
Linear regression of the null and full modelsfit_models fit_models,deSet-method
Fitted data from the full modelfitFull fitFull,deFit-method
Fitted data from the null modelfitNull fitNull,deFit-method
Matrix representation of full modelfullMatrix fullMatrix,deSet-method fullMatrix<- fullMatrix<-,deSet-method
Full model equationfullModel fullModel,deSet-method fullModel<- fullModel<-,deSet-method
Gene expression dataset from Idaghdour et al. (2008)gibson
Individuals sampled in experimentindividual individual,deSet-method individual<- individual<-,deSet-method
Gene expression dataset from Rodwell et al. (2004)kidney
Modular optimal discovery procedure (mODP)kl_clust kl_clust,deSet,deFit-method kl_clust,deSet,missing-method
Performs F-test (likelihood ratio test using Normal likelihood)lrt lrt,deSet,deFit-method lrt,deSet,missing-method
Matrix representation of null modelnullMatrix nullMatrix,deSet-method nullMatrix<- nullMatrix<-,deSet-method
Null model equation from deSet objectnullModel nullModel,deSet-method nullModel<- nullModel<-,deSet-method
The optimal discovery procedureodp odp,deSet,deFit-method odp,deSet,missing-method
Access/set qvalue slotqvalueObj qvalueObj,deSet-method qvalueObj<- qvalueObj<-,deSet-method
Residuals of full model fitresFull resFull,deFit-method
Residuals of null model fitresNull resNull,deFit-method
Show function for deFit and deSetshow show,deFit-method show,deSet-method
Statistic type used in analysissType sType,deFit-method
Summary of deFit and deSetsummary summary,deFit-method summary,deSet-method