affycoretools-package |
Make repetitive analyses of microarray and RNA-Seq data simpler with affycoretools. |
affycoretools |
Make repetitive analyses of microarray and RNA-Seq data simpler with affycoretools. |
affyLinks |
Add links to data when using ReportingTools |
affystart |
Pre-processing for Affymetrix Data |
annBM |
Select Available Annotation from a Biomart |
dataAndHeatmapPage |
A function to create an annotated HTML table for all genes in a significant gene set as well as a heatmap of these data. |
entrezLinks |
Add links to data when using ReportingTools |
foldFilt |
Output Fold Change Data |
foldFiltBM |
Output Fold Change Data using biomaRt |
geneSetPage |
A function to create an HTML page for each gene set, as well as the HTML pages for each significant gene set. |
getMainProbes |
Remove control probesets from ST arrays |
getUniqueLL |
Subset a Vector of Probesets |
goLinks |
Add links to data when using ReportingTools |
gsHeatmap |
A function to create a simple heatmap and key. |
hyperG2annaffy |
HTML tables from GOIDs |
hyperGoutput |
Output Tables Based on Hypergeometric Test |
limma2annaffy |
Function to Create HTML Tables from limma Objects |
limma2annaffy.na |
Function to Create HTML Tables from limma Objects |
limma2biomaRt |
Function to Create HTML Tables from limma Objects using biomaRt for Annotation |
limma2biomaRt.na |
Function to Create HTML Tables from limma Objects using biomaRt for Annotation |
linksBM |
Select Available Annotation from a Biomart |
makeHmap |
A function to create a heatmap-like object or matrix of correlations between miRNA and mRNA data. |
makeImages |
Add dotplot images |
makeVenn |
High-level function for making Venn diagrams and outputting the results from the diagrams in HTML and CSV files. |
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 romer on a set of contrasts. |
plotDeg |
Functions to Plot Density and RNA Degradation Plots |
plotHist |
Functions to Plot Density and RNA Degradation Plots |
plotPCA |
A Function to Make a PCA Plot from an ExpressionSet |
probes2table |
Convert Affy Probe ids to Annotated HTML Table |
probes2tableBM |
Convert Affy Probe ids to Annotated HTML Table using biomaRt |
runRomer |
A function to run the romer function on a set of contrasts. |
venn4Way |
4-way Venn Diagrams |
vennCounts2 |
Compute Counts for Venn Diagram |
vennPage |
High-level function for making Venn diagrams with clickable links to HTML pages with the underlying genes. |
vennSelect |
Select and Output Genelists Based on Venn Diagrams |
vennSelect2 |
Select and Output Genelists Based on Venn Diagrams |
vennSelectBM |
Select and Output Genelists Based on Venn Diagrams using biomaRt |
vennSelectFC |
Select and Output Gene Lists Based on Venn Diagrams |
writeFit |
Function to output annotated fit data from limma |