MetaIntegrator: Meta-Analysis of Gene Expression Data

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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>.

Author
Winston A. Haynes, Francesco Vallania, Aurelie Tomczak, Timothy Sweeney, Erika Bongen, Purvesh Khatri
Date of publication
2016-09-29 08:02:32
Maintainer
Winston A. Haynes <hayneswa@stanford.edu>
License
LGPL
Version
1.0.3
URLs

View on CRAN

Man pages

backwardSearch
Backward Search Function
calculateROC
Calculate ROC Curve Statistics
calculateScore
Calculate a signature Z-score for a set of genes in a single...
checkDataObject
Check for errors in objects used for analysis
ens_ensgID_table
ENSEMBL gene id table cache
ens_entrez_table
ENSEMBL entrez table cache
filterGenes
Filter out significant genes from meta-analysis results
forestPlot
Compare effect sizes of a gene across all datasets in...
forwardSearch
Forward Search Function
getGEOData
GEO download/processing through GEOquery
getMostRecentFilter
Get name of most recent filter
getSampleLevelGeneData
Extract gene-level data from a given data object
heatmapPlot
Generates a heatmap with effect sizes for all genes which...
metaIntegrator_public-package
MetaIntegrator package for meta-analysis of gene expression...
regressionPlot
Generate a plot which draws a regrssion line between the Meta...
rocPlot
Plot ROC Curve for a Dataset
runMetaAnalysis
Run the meta-analysis algorithm
summarizeFilterResults
Summarize the filtered analysis results
tinyMetaObject
A Tiny MetaObject
ucsc_genbank_table
UCSC genbank table cache
ucsc_refseq_table
UCSC refseq table cache
violinPlot
Compare groups within a single dataset in a violin plot

Files in this package

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