# Reference

## DTU functions

Differential Transcript Usage analysis methods

`import_gtf()` | Parse a `GTF` file and return a dataframe of specified features.
`import_counts()` | Import quantification results
`combine_to_matrix()` | Combine sparse matrices.
`run_drimseq()` | Main filtering and DTU statistical computations
`posthoc_and_stager()` | Posthoc filtering and two-staged statistical tests
`priming_bias_detection_probability()` | Estimate transcript detection probability

## DGE functions

Basic Differential Gene Expression analysis pipeline

`import_dge_counts()` | Import quantification results for DGE analysis
`combine_to_matrix()` | Combine sparse matrices.
`run_deseq2()` | Perform DGE analysis

## Visualization functions

Aggregate and visualize results

`create_dtu_table()` | Summarize DTUrtle results
`plot_dimensional_reduction()` | Visualize data in dimensional reduction coordinates
`plot_dtu_table()` | Plot a DTU table to HTML and image
`plot_proportion_barplot()` | Visualize as barplot
`plot_proportion_pheatmap()` | Visualize as extended heatmap
`plot_transcripts_view()` | Visualize transcripts on genomic scale

## Column formatters

Formatter functions for `plot_dtu_table()`

`table_percentage_bar()` | Column formatter for percentages
`table_pval_tile()` | Column formatter for p-values

## Utility functions

Help with data processing

`dataframe_to_partitioning()` | Convert a data frame to a partitioning list.
`get_by_partition()` | Aggregate data frame by partitions
`get_proportion_matrix()` | Compute proportion matrix
`move_columns_to_front()` | Reorder columns
`one_to_one_mapping()` | Ensure one-to-one mapping
`partitioning_to_dataframe()` | Convert a partitioning list to a data frame.
`rm_version()` | Remove ensembl version number
`summarize_to_gene()` | Summarize matrix to gene level