RNApysoforms documentation

Welcome to the documentation for the RNApysoforms package. Below are the key functions included in this library.

Functions Overview

RNApysoforms.calculate_exon_number(annotation)	Assigns exon numbers to exons, CDS, and introns within a genomic annotation dataset based on transcript structure and strand direction.
RNApysoforms.gene_filtering(target_gene, ...)	Filters genomic annotations and optionally an expression matrix for a specific gene, with options to order and select top expressed transcripts.
RNApysoforms.make_plot(traces[, ...])	Creates a multi-panel Plotly figure combining transcript structure plots and expression data plots.
RNApysoforms.make_traces([annotation, ...])	Generates Plotly traces for visualizing transcript structures and expression data.
RNApysoforms.process_ensembl_gtf(gtf_df)	Processes an already-loaded GTF DataFrame to extract and format genomic features.
RNApysoforms.process_expression_matrix(...)	Processes an expression matrix DataFrame, optionally merging with metadata, performing CPM normalization, and calculating relative transcript abundance.
RNApysoforms.read_expression_matrix(...[, ...])	Loads and processes an expression matrix, optionally merging with metadata, performing CPM normalization, and calculating relative transcript abundance.
RNApysoforms.read_ensembl_gtf(path)	Reads a GTF (Gene Transfer Format) file and returns the data as a Polars DataFrame.
RNApysoforms.shorten_gaps(annotation[, ...])	Shortens intron and transcript start gaps between exons in genomic annotations to enhance visualization.
RNApysoforms.to_intron(annotation[, ...])	Converts exon coordinates into corresponding intron coordinates within a genomic annotation dataset.

Vignettes:

• Basic usage (quick start)
• Rescaled introns
• Expression plot
• Expression plot with metadata
• Expression plot normalized, filtered, and ordered
• Plot specific transcripts
• Use custom color palette for plotting
• Use consistent color maps for making your plots
• Separate CDS interactivity
• Auto rescale plots
• Dealing with non-ENSEMBL GTF files
• Making expression plot only
• Making custom ajustments to figure
• Violin expression plot
• Using transcript_name instead of transcript_id
• Saving plots
• Annotate RNA modification sites of interest or other single nucleotide sites of interest

Changelog:

• Change Log