r-other-chbutils

GNU R utilities from Harvard School of Public Health Bioinformatics

Description

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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Homepage

https://github.com/hbc/CHBUtils

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