Introduction | Installation | Data input | Alternative 1 -- Tab-delimited Text Files | Alternative 2 -- Multiple table objects | Alternative 3 -- Results from limma | Alternative 4 -- Ideal input data (for tests only) | Input data post-processing (optional) | Numeric table correcting | Filtering values below statistical significance | Renaming the row names | SV Analyses | Summarization | Makes a safe copy of the summary data | Appends the quantiles data | Appends the clustered data | Draws a SV plot with grouped highlights (optional) | Alternative 2 -- With factors | Shortcut function and reanalysis
Package: geva 1.21.0
Itamar José Guimarães Nunes
geva: Gene Expression Variation Analysis (GEVA)
Statistic methods to evaluate variations of differential expression (DE) between multiple biological conditions. It takes into account the fold-changes and p-values from previous differential expression (DE) results that use large-scale data (*e.g.*, microarray and RNA-seq) and evaluates which genes would react in response to the distinct experiments. This evaluation involves an unique pipeline of statistical methods, including weighted summarization, quantile detection, cluster analysis, and ANOVA tests, in order to classify a subset of relevant genes whose DE is similar or dependent to certain biological factors.
Authors:
geva_1.21.0.tar.gz
geva_1.21.0.zip(r-4.7)geva_1.21.0.zip(r-4.6)geva_1.21.0.zip(r-4.5)
geva_1.21.0.tgz(r-4.6-any)geva_1.21.0.tgz(r-4.5-any)
geva_1.21.0.tar.gz(r-4.7-any)geva_1.21.0.tar.gz(r-4.6-any)
geva_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
geva/json (API)
| # Install 'geva' in R: |
| install.packages('geva', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/sbcblab/geva/issues
On BioConductor:geva-1.21.0(bioc 3.24)geva-1.20.0(bioc 3.23)
classificationdifferentialexpressiongeneexpressionmicroarraymultiplecomparisonrnaseqsystemsbiologytranscriptomics
Last updated from:bbc8940ea2. Checks:1 WARNING, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 235 | ||
| linux-devel-x86_64 | OK | 295 | ||
| source / vignettes | OK | 328 | ||
| linux-release-x86_64 | OK | 272 | ||
| macos-release-arm64 | OK | 188 | ||
| macos-oldrel-arm64 | OK | 169 | ||
| windows-devel | OK | 236 | ||
| windows-release | OK | 217 | ||
| windows-oldrel | OK | 217 | ||
| wasm-release | OK | 171 |
Exports:analysis.paramsas.SVTablecentroidsclassification.tableclassification.table<-cluster.methodelem.classelem.class<-factorsfactors<-featureTablefeatureTable<-get.distance.methodget.summary.methodget.variation.methodgeva.clustergeva.dclustergeva.finalizegeva.hclustergeva.ideal.examplegeva.input.correctgeva.input.filtergeva.input.rename.rowsgeva.merge.inputgeva.quantilesgeva.quickgeva.read.tablesgeva.summarizegroup.relsgroupsgroupsetsgroupsets<-infolistinfolist<-inputdatainputnamesinputvaluesinputweightsoffsetsoptions.cl.score.methodoptions.cluster.methodoptions.dcluster.methodoptions.distanceoptions.factoring.p.adjustoptions.hc.methodoptions.hc.metricoptions.quantilesoptions.summaryoptions.variationplotqareasizesqcountqindexesquantilesquantiles.methodresults.tablescoresshowsvsv.datasv.scoressvattrsvtabletop.genestyped.listvariation
Dependencies:dbscanfastclustergenericsmatrixStatsRcpp
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| GEVA Generic Methods | analysis.params as.SVTable centroids classification.table classification.table<- cluster.method elem.class elem.class<- factors factors<- featureTable featureTable<- generics get.distance.method get.summary.method get.variation.method group.rels groups groupsets groupsets<- infolist infolist<- inputdata inputnames inputvalues inputweights offsets qareasizes qcount qindexes quantiles quantiles.method results.table scores sv sv.data sv.scores svattr variation |
| GEVA Cluster Analysis | geva.cluster options.cl.score.method options.cluster.method options.distance |
| GEVA Density Clustering | geva.dcluster options.dcluster.method |
| Concatenating GEVA calculations into the final results | geva.finalize options.factoring.p.adjust |
| GEVA Hierarchical Clustering | geva.hcluster options.hc.method options.hc.metric |
| GEVA ``Ideal'' Example for Package Testing | geva.ideal.example |
| GEVA Input Post-processing | geva.input.correct geva.input.filter geva.input.rename.rows |
| GEVA Input Processing and Merge | geva.merge.input geva.read.tables |
| GEVA Quantiles Detection | geva.quantiles options.quantiles |
| All-In-One Function for GEVA Intermediate Procedures | geva.quick |
| Summarizes the GEVAInput | geva.summarize options.summary options.variation |
| GEVA Clustering Results | cluster.method,GEVACluster-method GEVACluster-class lines.GEVACluster plot,GEVACluster,SVTable-method show,GEVACluster-method |
| GEVA Grouped Summary-Variation Table | analysis.params,GEVAGroupedSummary-method as.expression.GEVAGroupedSummary as.matrix.GEVAGroupedSummary cluster.method,GEVAGroupedSummary-method GEVAGroupedSummary-class groupsets,GEVAGroupedSummary-method groupsets<-,GEVAGroupedSummary,GEVAGroupSet-method lines.GEVAGroupedSummary plot,GEVAGroupedSummary,missing-method points.GEVAGroupedSummary quantiles,GEVAGroupedSummary-method show,GEVAGroupedSummary-method |
| GEVA Grouping Results | analysis.params,GEVAGroupSet-method as.data.frame.GEVAGroupSet as.expression.GEVAGroupSet as.SVTable.GEVAGroupSet centroids,GEVAGroupSet-method classification.table,GEVAGroupSet-method classification.table<-,GEVAGroupSet,data.frame-method cluster.method,GEVAGroupSet-method color.values.GEVAGroupSet featureTable,GEVAGroupSet-method GEVAGroupSet-class groups,GEVAGroupSet-method infolist,GEVAGroupSet,character-method infolist,GEVAGroupSet,missing-method infolist<-,GEVAGroupSet,list-method length,GEVAGroupSet-method levels.GEVAGroupSet names,GEVAGroupSet-method offsets,GEVAGroupSet-method plot,GEVAGroupSet,GEVAGroupSet-method plot,GEVAGroupSet,missing-method plot,GEVAGroupSet,SVTable-method plot,SVTable,GEVAGroupSet-method points.GEVAGroupSet scores,GEVAGroupSet,character-method scores,GEVAGroupSet,missing-method show,GEVAGroupSet-method sv,GEVAGroupSet-method sv.data,GEVAGroupSet-method |
| GEVA Input Data | analysis.params,GEVAInput-method as.array.GEVAInput dim,GEVAInput-method dimnames,GEVAInput-method dimnames<-,GEVAInput,list-method factors,GEVAInput-method factors<-,GEVAInput,character-method factors<-,GEVAInput,factor-method featureTable,GEVAInput-method featureTable<-,GEVAInput,data.frame-method GEVAInput-class head.GEVAInput infolist,GEVAInput,character-method infolist,GEVAInput,missing-method infolist<-,GEVAInput,list-method inputdata,GEVAInput-method inputnames,GEVAInput-method inputvalues,GEVAInput-method inputweights,GEVAInput,logical-method inputweights,GEVAInput,missing-method length,GEVAInput-method levels.GEVAInput names,GEVAInput-method plot,GEVAInput,missing-method show,GEVAInput-method tail.GEVAInput [,GEVAInput,ANY,ANY,ANY-method |
| GEVA Quantiles Grouping Results | as.expression.GEVAQuantiles as.SVTable.GEVAQuantiles classification.table,GEVAQuantiles-method classification.table<-,GEVAQuantiles,data.frame-method cluster.method,GEVAQuantiles-method dim,GEVAQuantiles-method GEVAQuantiles-class lines.GEVAQuantiles plot,GEVAQuantiles,SVTable-method qareasizes,GEVAQuantiles-method qcount,GEVAQuantiles-method qindexes,GEVAQuantiles-method quantiles,GEVAQuantiles-method quantiles.method,GEVAQuantiles-method show,GEVAQuantiles-method sv.scores,GEVAQuantiles-method [,GEVAQuantiles,ANY,ANY,ANY-method |
| GEVA Adjusted Quantiles Results | GEVAQuantilesAdjusted-class group.rels,GEVAQuantilesAdjusted-method show,GEVAQuantilesAdjusted-method |
| GEVA Results Table | $,GEVAResults-method analysis.params,GEVAResults-method as.expression.GEVAResults dim,GEVAResults-method dimnames,GEVAResults-method featureTable,GEVAResults-method GEVAResults-class head.GEVAResults infolist,GEVAResults,character-method infolist,GEVAResults,missing-method inputdata,GEVAResults-method inputvalues,GEVAResults-method inputweights,GEVAResults,logical-method inputweights,GEVAResults,missing-method length,GEVAResults-method levels.GEVAResults names,GEVAResults-method plot,GEVAResults,missing-method points.GEVAResults quantiles,GEVAResults-method results.table,GEVAResults-method show,GEVAResults-method sv,GEVAResults-method sv.data,GEVAResults-method [,GEVAResults,ANY,ANY,ANY-method |
| GEVA Summary-Variation Table | analysis.params,GEVASummary-method as.expression.GEVASummary as.matrix.GEVASummary factors,GEVASummary-method factors<-,GEVASummary,character-method factors<-,GEVASummary,factor-method featureTable,GEVASummary-method get.summary.method.GEVASummary get.variation.method.GEVASummary GEVASummary-class groupsets,GEVASummary-method groupsets<-,GEVASummary,GEVAGroupSet-method groupsets<-,GEVASummary,TypedList-method infolist,GEVASummary,missing-method infolist<-,GEVASummary,list-method inputdata,GEVASummary-method inputnames,GEVASummary-method inputvalues,GEVASummary-method inputweights,GEVASummary,logical-method inputweights,GEVASummary,missing-method plot,GEVASummary,missing-method quantiles,GEVASummary-method show,GEVASummary-method |
| Summary-Variation Attribute Field | $,SVAttribute-method as.character.SVAttribute as.vector.SVAttribute dim,SVAttribute-method names,SVAttribute-method show,SVAttribute-method summary.SVAttribute sv,SVAttribute-method sv.data,SVAttribute-method svattr,character,character-method svattr,integer,integer-method svattr,numeric,numeric-method SVAttribute SVAttribute-class SVChrAttribute SVChrAttribute-class SVIntAttribute SVIntAttribute-class SVNumAttribute SVNumAttribute-class variation.SVAttribute [,SVAttribute,ANY,ANY,ANY-method |
| Summary-Variation Table | $,SVTable-method as.data.frame.SVTable as.matrix.SVTable as.SVTable.data.frame as.SVTable.matrix as.SVTable.SVTable dim,SVTable-method dimnames,SVTable-method format.SVTable head.SVTable is.na.SVTable length,SVTable-method names,SVTable-method plot,SVTable,missing-method points.SVTable show,SVTable-method summary.SVTable sv,SVTable-method sv.data,SVTable-method SVTable svtable SVTable-class tail.SVTable variation.SVTable with.SVTable [,SVTable,ANY,ANY,ANY-method |
| Top Results from GEVA | top.genes |
| Type-strict List (TypedList-class) | as.list.TypedList as.typed.list.list as.typed.list.TypedList as.typed.list.vector elem.class,TypedList-method elem.class<-,TypedList,character-method show,TypedList-method typed.list TypedList-class [,TypedList,ANY,missing,missing-method [<-,TypedList,character,missing-method |
