Changelog

Source: NEWS.md

Isoformic 0.1.3 (Development Version)

Release Date: Unreleased

Development Changelog: dev

Added

• New output_path = ":cache:" to store downloaded reference files in a dedicated cache folder. This is the new default behavior for download_reference().

• New get_isoformic_cache() function to retrieve the path to the cache folder.

• New IsoformicExperiment class to encapsulate all workflow inputs with a disk-based backend and tidy interface.

• New generics and methods for the IsoformicExperiment class:

  • col_data() - Retrieve Sample Metadata

  • row_data() - Retrieve Metadata for Transcripts in the Assay Data

  • annot_data() - Retrieve Aggregated Annotation Data (transcript-centric)

  • annot_data_transcripts() - Retrieve Transcript Annotation Data

  • annot_data_genes() - Retrieve Gene Annotation Data

  • annot_data_exons() - Retrieve Exon Annotation Data

  • tx_to_gene() - Retrieve Transcript to Gene Mapping from the Annotation

  • summarize_to_gene() - Summarize Transcript-level Expression to Gene-level

  • de_tx() - Retrieve Differential Expression Results for Transcripts

  • de_gene() - Retrieve Differential Expression Results for Genes

• New interface for plot_log2fc() function to visualize log2 fold changes of transcripts within a gene.

• New feature_column argument in plot_log2FC() to specify the column name in the DE results table that contains the feature names (e.g., gene or transcript names).

• New file_type = "genome_fasta" option in download_reference() to download the genome FASTA file from GENCODE.

Changed

• Argument file_type in download_reference() is now "gff" by default.
• Default GENCODE version in download_reference() is now "49" by default.
• Argument output_path in download_reference() is now ":cache:".
• Arguments DEG_DET_table and selected_genes in plot_log2FC() are now de_data and feature.

Isoformic 0.1.2

Release Date: 2025-10-06

Development Changelog: 0.1.2

Added

• New DuckDB based parse_annotation().
• New plot_genomic_context() function to visualize the genomic context of a gene with its transcripts.
• New tx_type_palette() function to provide a default color palette for transcript types.

Fixed

• In make_tx_to_gene() output, wrong column name entrez_id replaced for tx_length.

Isoformic 0.1.1

Release Date: 2024-06-18

Development Changelog: 0.1.1

Added

• download_reference(): now supports organism = c("human", "mouse"), with organism = "human" being the default.
• download_reference(): argument file_type = "gtf" is the default.
• prepare_annotation(): Parse both GTF and GFF file formats into required annotation data.

Fixed

• prepare_profile_data(): accepts matrix and data.frame as input for the txi_transcript argument.

Isoformic 0.1.0

Release Date: 2024-06-11

Development Changelog: 0.1.0

Added

• Release of the initial workflow.

Isoformic 0.0.1

Release Date: 2024-06-08

Development Changelog: 0.0.1

Added

• Original workflow style code added.