Changes in version 0.1.3                        

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.

                        Changes in version 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.

                        Changes in version 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.

                        Changes in version 0.1.0                        

Release Date: 2024-06-11

Development Changelog: 0.1.0

Added

  - Release of the initial workflow.

                        Changes in version 0.0.1                        

Release Date: 2024-06-08

Development Changelog: 0.0.1

Added

  - Original workflow style code added.