Transcriptome analysis is a widely used method in biological sciences, providing insights into gene expression and regulation. However, analyzing transcriptomes at the gene level can be misleading as genes often undergo alternative splicing, leading to the production of multiple transcript types from the same gene. These transcripts can be productive, generating different isoforms of the same protein, or unproductive.
We present Isoformic (https://github.com/luciorq/isoformic), an R-based pipeline for analyzing transcript-level results from short-read RNA-seq, applicable to any well-annotated transcriptome. Isoformic enables users to extract transcript types, identify genes with differentially expressed transcripts, visualize relative fold changes of transcripts between conditions, compare intron/exon composition of transcripts, and enrich transcripts with a selected gene set separated by transcript type. The package consolidates commonly used visualization types and provides user-friendly functions for exploring biologically relevant information. Isoformic offers a customizable and straightforward workflow for analyzing transcript-level findings from bulk transcriptomic data.