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[ Source: r-other-chbutils  ]

Package: r-other-chbutils (0.1+git20171026.a226cee-2)

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GNU R utilities from Harvard School of Public Health Bioinformatics

This GNU R package contains the following functions:

 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
                       Plots the differntially expressed genes on an MA
 plotDE                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
                       Plots the pvalue quantiles against the uniform
 qqplot_JH             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

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