MetaIntegrator: Meta-Analysis of Gene Expression Data

A pipeline for the meta-analysis of gene expression data. We have assembled several analysis and plot functions to perform integrated multi-cohort analysis of gene expression data (meta- analysis). Methodology described in: <http://biorxiv.org/content/early/2016/08/25/071514>.

AuthorWinston A. Haynes, Francesco Vallania, Aurelie Tomczak, Timothy Sweeney, Erika Bongen, Purvesh Khatri
Date of publication2016-09-29 08:02:32
MaintainerWinston A. Haynes <hayneswa@stanford.edu>
LicenseLGPL
Version1.0.3
http://biorxiv.org/content/early/2016/08/25/071514

View on CRAN

Functions

backwardSearch Man page
calculateROC Man page
calculateScore Man page
checkDataObject Man page
ens_ensgID_table Man page
ens_entrez_table Man page
filterGenes Man page
forestPlot Man page
forwardSearch Man page
getGEOData Man page
getMostRecentFilter Man page
getSampleLevelGeneData Man page
heatmapPlot Man page
MetaIntegrator Man page
regressionPlot Man page
rocPlot Man page
runMetaAnalysis Man page
summarizeFilterResults Man page
tinyMetaObject Man page
ucsc_genbank_table Man page
ucsc_refseq_table Man page
violinPlot Man page

Files

MetaIntegrator
MetaIntegrator/inst
MetaIntegrator/inst/CITATION
MetaIntegrator/inst/doc
MetaIntegrator/inst/doc/MetaIntegrator.R
MetaIntegrator/inst/doc/MetaIntegrator.html
MetaIntegrator/inst/doc/MetaIntegrator.Rmd
MetaIntegrator/inst/unitTests
MetaIntegrator/inst/unitTests/testOutput
MetaIntegrator/inst/unitTests/testOutput/temp.temp
MetaIntegrator/inst/unitTests/test_backwardSearch.R
MetaIntegrator/inst/unitTests/test_rocPlot.R
MetaIntegrator/inst/unitTests/test_filterGenes.R
MetaIntegrator/inst/unitTests/goldStandardOutput
MetaIntegrator/inst/unitTests/goldStandardOutput/violinPlots.pdf
MetaIntegrator/inst/unitTests/goldStandardOutput/rocPlots.pdf
MetaIntegrator/inst/unitTests/goldStandardOutput/forestPlots.pdf
MetaIntegrator/inst/unitTests/test_forwardSearch.R
MetaIntegrator/inst/unitTests/test_checkDataObject.R
MetaIntegrator/inst/unitTests/test_summarizeFilterResults.R
MetaIntegrator/inst/unitTests/test_calculateROC.R
MetaIntegrator/inst/unitTests/test_getSampleLevelGeneData.R
MetaIntegrator/inst/unitTests/test_getMostRecentFilter.R
MetaIntegrator/inst/unitTests/test_runMetaAnalysis.R
MetaIntegrator/inst/unitTests/test_forestPlot.R
MetaIntegrator/inst/unitTests/test_calculateScore.R
MetaIntegrator/inst/unitTests/test_violinPlot.R
MetaIntegrator/tests
MetaIntegrator/tests/runTests.R
MetaIntegrator/NAMESPACE
MetaIntegrator/NEWS
MetaIntegrator/data
MetaIntegrator/data/ucsc_refseq_table.rda
MetaIntegrator/data/ucsc_genbank_table.rda
MetaIntegrator/data/tinyMetaObject.RData
MetaIntegrator/data/datalist
MetaIntegrator/data/ens_entrez_table.rda
MetaIntegrator/data/ens_ensgID_table.rda
MetaIntegrator/R
MetaIntegrator/R/ROC_and_search_functions.R MetaIntegrator/R/checkDataObject.R MetaIntegrator/R/metaIntegrator_public.R MetaIntegrator/R/metaAnalysis.R MetaIntegrator/R/summarizeFilterResults.R MetaIntegrator/R/getMostRecentFilter.R MetaIntegrator/R/heatmapPlot.R MetaIntegrator/R/getGEOData.R MetaIntegrator/R/calculateScore.R MetaIntegrator/R/checkDataObject_functions.R MetaIntegrator/R/filterGenes.R MetaIntegrator/R/metaAnalysisFoundation.R MetaIntegrator/R/runMetaAnalysis.R MetaIntegrator/R/violinPlot.R MetaIntegrator/R/regressionPlot.R MetaIntegrator/R/forestPlot.R MetaIntegrator/R/getSampleLevelGeneData.R
MetaIntegrator/vignettes
MetaIntegrator/vignettes/images
MetaIntegrator/vignettes/images/Eq3.png
MetaIntegrator/vignettes/images/Eq1.png
MetaIntegrator/vignettes/images/schema_simplified.pdf
MetaIntegrator/vignettes/images/schema_simplified2.png
MetaIntegrator/vignettes/images/Eq4.png
MetaIntegrator/vignettes/images/Eq2.png
MetaIntegrator/vignettes/MetaIntegrator.Rmd
MetaIntegrator/README.md
MetaIntegrator/MD5
MetaIntegrator/build
MetaIntegrator/build/vignette.rds
MetaIntegrator/DESCRIPTION
MetaIntegrator/man
MetaIntegrator/man/getGEOData.Rd MetaIntegrator/man/calculateScore.Rd MetaIntegrator/man/checkDataObject.Rd MetaIntegrator/man/runMetaAnalysis.Rd MetaIntegrator/man/regressionPlot.Rd MetaIntegrator/man/ucsc_genbank_table.Rd MetaIntegrator/man/ens_ensgID_table.Rd MetaIntegrator/man/summarizeFilterResults.Rd MetaIntegrator/man/ucsc_refseq_table.Rd MetaIntegrator/man/forwardSearch.Rd MetaIntegrator/man/backwardSearch.Rd MetaIntegrator/man/getMostRecentFilter.Rd MetaIntegrator/man/forestPlot.Rd MetaIntegrator/man/ens_entrez_table.Rd MetaIntegrator/man/rocPlot.Rd MetaIntegrator/man/tinyMetaObject.Rd MetaIntegrator/man/heatmapPlot.Rd MetaIntegrator/man/violinPlot.Rd MetaIntegrator/man/calculateROC.Rd MetaIntegrator/man/getSampleLevelGeneData.Rd MetaIntegrator/man/metaIntegrator_public-package.Rd MetaIntegrator/man/filterGenes.Rd

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