affycoretools: Functions useful for those doing repetitive analyses with Affymetrix GeneChips

Various wrapper functions that have been written to streamline the more common analyses that a core Biostatistician might see.

Author
James W. MacDonald
Date of publication
None
Maintainer
James W. MacDonald <jmacdon@u.washington.edu>
License
Artistic-2.0
Version
1.46.1

View on Bioconductor

Man pages

affycoretools
Make repetitive analyses of microarray and RNA-Seq data...
affycoretools-defunct
Defunct functions in package 'affycoretools'
affystart
Pre-processing for Affymetrix Data
annotateEset
Method to annotate ExpressionSets automatically
dataAndHeatmapPage
A function to create an annotated HTML table for all genes in...
entrezLinks
Add links to data when using ReportingTools
fixHeaderAndGo
Fix data.frame header for use with ReportingTools
geneSetPage
A function to create an HTML page for each gene set, as well...
getCols
Correct Ordering of Contrasts
getMainProbes
Remove control probesets from ST arrays
gsHeatmap
A function to create a simple heatmap and key.
intNames
Create Names for Venn Diagram Intersections
make.cl
A Function to Make a Classlabel Vector for Plotting
makeGoGeneTable
Make Gene table from GO analysis results
makeGoTable
Create HTML tables for Gene Ontology (GO) analyses
makeHmap
A function to create a heatmap-like object or matrix of...
makeImages
Add dotplot images
makeIndices
Create Indices for Venn Diagrams
makeVenn
High-level function for making Venn diagrams and outputting...
maplot
A Function to make MA plots from all arrays.
mirna2mrna
A function to map miRNA to mRNA.
outputRomer
A function to create HTML output from the results of running...
pca.legend
A Function to Automagically Place a Legend in a PCA Plot
plotDeg
Functions to Plot Density and RNA Degradation Plots
plotPCA
A Function to Make a PCA Plot from an ExpressionSet
runRomer
A function to run the romer function on a set of contrasts.
tableFilt
Filter a topTable object
venn4Way
4-way Venn Diagrams
vennCounts2
Compute Counts for Venn Diagram
vennPage
High-level function for making Venn diagrams with clickable...
vennSelect2
Select and Output Genelists Based on Venn Diagrams
writeFit
Function to output annotated fit data from limma

Files in this package

affycoretools/DESCRIPTION
affycoretools/NAMESPACE
affycoretools/NEWS
affycoretools/R
affycoretools/R/Defunct.R
affycoretools/R/affycoretools.R
affycoretools/R/affystart.R
affycoretools/R/annotateEset.R
affycoretools/R/geneSetTables.R
affycoretools/R/mirnaFuns.R
affycoretools/R/plotma.R
affycoretools/R/reportingTools.R
affycoretools/R/vennSelect.R
affycoretools/R/zzz.R
affycoretools/README.md
affycoretools/build
affycoretools/build/vignette.rds
affycoretools/inst
affycoretools/inst/doc
affycoretools/inst/doc/RefactoredAffycoretools.R
affycoretools/inst/doc/RefactoredAffycoretools.Rnw
affycoretools/inst/doc/RefactoredAffycoretools.pdf
affycoretools/inst/examples
affycoretools/inst/examples/Statistical_analysis.Rnw
affycoretools/inst/examples/Statistical_analysis.bib
affycoretools/man
affycoretools/man/affycoretools-defunct.Rd
affycoretools/man/affycoretools.Rd
affycoretools/man/affystart.Rd
affycoretools/man/annotateEset.Rd
affycoretools/man/dataAndHeatmapPage.Rd
affycoretools/man/entrezLinks.Rd
affycoretools/man/fixHeaderAndGo.Rd
affycoretools/man/geneSetPage.Rd
affycoretools/man/getCols.Rd
affycoretools/man/getMainProbes.Rd
affycoretools/man/gsHeatmap.Rd
affycoretools/man/intNames.Rd
affycoretools/man/make.cl.Rd
affycoretools/man/makeGoGeneTable.Rd
affycoretools/man/makeGoTable.Rd
affycoretools/man/makeHmap.Rd
affycoretools/man/makeImages.Rd
affycoretools/man/makeIndices.Rd
affycoretools/man/makeVenn.Rd
affycoretools/man/maplot.Rd
affycoretools/man/mirna2mrna.Rd
affycoretools/man/outputRomer.Rd
affycoretools/man/pca.legend.Rd
affycoretools/man/plotDeg.Rd
affycoretools/man/plotPCA.Rd
affycoretools/man/runRomer.Rd
affycoretools/man/tableFilt.Rd
affycoretools/man/venn4Way.Rd
affycoretools/man/vennCounts2.Rd
affycoretools/man/vennPage.Rd
affycoretools/man/vennSelect2.Rd
affycoretools/man/writeFit.Rd
affycoretools/vignettes
affycoretools/vignettes/RefactoredAffycoretools.Rnw
affycoretools/vignettes/abatch.Rdata
affycoretools/vignettes/exprSet.Rdata
affycoretools/vignettes/exprSet2.Rdata
affycoretools/vignettes/pdata.txt