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| chb_utils-package | chb_utils |
| 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). |
| PCAplot.cds | Pairwise Principal Component Analysis Plots of CountDataSet objects |
| PCAplot.eset | Pairwise Principal Component Analysis Plots |
| 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 |