# Differential Expression Analysis of RNA-Seq Data

## Documentation for package ‘diffwrap’ version 0.6-3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

correlogram_pheatmap | Function to create a correlogram pheatmap, i.e., a plot to check randomness in the data set.
diffExpr | Main wrapper for executing the entire pipeline from reading in expression data such as count files to producing text files and graphs
diffr_expr_generate_cleaned_de_table_output | Helper function to generate an output table with only most relevant columns
diffr_pheatmap | Function to create a heatmap from differential gene expression values
diffr_venn | Function to produce a Venn diagram of differentially expressed gene tables
diffwrap | Differential expression analysis of RNA-Seq data
diffwrap_counts | Simulated RNA-Seq read counts for the package examples
diffwrap_samp_info | Sample sheet accompanying the simulated example counts
diff_expr_3d_scatterplot | Function to generate a 3D scatterplot
diff_expr_biomart | Function to retrieve additional information from biomart
diff_expr_dendro_plot | Function to generate dendrogram plots based on hierarchical clustering
diff_expr_extract_contrasts | Function to extract contrasts and generate top tables and plots
diff_expr_filter_counts | Function to filter counts
diff_expr_fit | Function to compute linear model fit and optionally apply 'voom' beforehand
diff_expr_get_samp_info | Function to standardize samp.info sample information data frame
diff_expr_ggplot_mds | Function to generate a MDS plot using 'ggplot2'
diff_expr_make_contrasts | Function to make contrast matrix
diff_expr_make_design | Function to create design matrix
diff_expr_ma_plot | Function to generate a M-A plot using 'ggplot2'
diff_expr_mds_plot | Wrapper around 'limma::plotMDS' to generate a MDS plot
diff_expr_PCA | Function to do PCA using 'stats::prcomp'
diff_expr_PCA_ggbiplot | Function to generate a PCA biplot using 'ggbiplot.n', a version of 'ggbiplot' from https://github.com/vqv/ggbiplot.
diff_expr_PCA_ggplot | Function to generate an ordinary two-dimensional PCA plot using 'ggplot2'
diff_expr_pseudo_counts | Function to calculate pseudo counts representing batch-corrected normalised but untransformed values
diff_expr_pval_hist_plot | Function to generate a histogram of the P-Value distribution
diff_expr_QC_plots | Main wrapper function for QC plots
diff_expr_read_counts | Function to read counts as produced by htseq-count
diff_expr_volcano_plot | Function to generate a Volcano plot using 'ggplot2'
format_ensembl_ids_annotated_to_term | Helper function for formatting the gene ID column of enrichment data frame.
get_hm_breaks | Function to define breaks to be used for changing the palette of the heatmap.
get_hm_colors | Function to compute colour palettes to be used in the heatmap.
ggbiplot.n | Make a biplot of PCA output data using ggplot2.
make_pheatmap_anno_color | Function to create the annotation colour list used in the heatmap
pheatmap_plots | Function to generate heatmap of gene expression values
plot_enrichment_network | Function for making network visualisation based on enrichment result, DE gene table and thresholding. Can take the input tables either as data frames or Excel files
prepare_scale_for_legend | Helper function for enrichment visualisations: prepare plot legend y coordinates and labels
prepare_volcano_of_given_property | Helper function that returns a volcano plot.
quantile_breaks | Function to define quantile breaks to be used for changing the palette of the heatmap.
reorderFactors | Function which reorders the levels of a column of a data frame specified as a factor
run.topGO | Function to run GO term enrichment analysis using the 'topGO' package.
runEnrichmentAnalyses | Wrapper for executing various enrichment analyses
run_clusterProfiler_GO | Runs clusterProfiler GO enrichment function for a DEG list or for a ranked gene list.
run_clusterProfiler_KEGG | Runs clusterProfiler KEGG enrichment function for a DEG list or for a ranked gene list.
run_gprofiler | Runs gprofiler function for a DEG list or for a ranked gene list.