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