PCAplot.cds             Pairwise Principal Component Analysis Plots of
                        CountDataSet objects
PCAplot.eset            Pairwise Principal Component Analysis Plots
annotate_df             Annotate Dataframe containing Ensembl IDs with
                        Gene Symbols and Descriptions
boxplotoutliers         Cel file IDs of intensity boxplot outlier
                        arrays (in characters).
chb_utils               chb_utils
col2rownames            add a column to a dataframe consisting of the
                        current rownames
convertIDs              Get other Ids for genes in the same order
create_report           Create report of QC
getTFpairs              Get mouse TF-target pairs from opossum database
get_biomart             Get biomart annotation from id
ggheatmap               generate a heatmap + dendrograms, ggplot2 style
ggheatmap.show          Display a ggheatmap
ggplotDispEsts          Plot Dispersion Estimates - nicer ggplot
                        version of DESeq graph
mds                     Plot MDS
mdsplot.RGset           MDS (MultiDimensional Scaling) Plots
nuseoutliers            Cel file IDs of intensity NUSE outlier arrays
                        (in characters).
plotDE                  Plots the differntially expressed genes on an
                        MA plot, ggplot style If adjusted pvalues are
                        present, colors those that pass cutoff red
plot_dendro             ggplot based dendrogram plot
print_enrichGO          Clean and print results from enrichGO
qqplot_JH               Plots the pvalue quantiles against the uniform
                        distribution. If adjusted pvalues are present,
                        colors those that pass cutoff red
rleoutliers             Cel file IDs of intensity RLE outlier arrays
                        (in characters).
row2colnames            add a column to a dataframe consisting of the
                        current rownames
runGO                   Run GO using clusterprofiler
variance_by_component   Plot PC importance
volcano_density_plot    Create volcano plot from log2FC and adjusted
                        pvalues data frame
write_report            Write report of QC
