Changes in version 1.3.5                        

  - Fix a bug in maploss calculation in make_subTxDb_from_GTF.
      - Fix user-genome issue in make_subTxDb_from_GTF

                        Changes in version 1.3.4                        

  - Modify pseudo count for ratio matrix

                        Changes in version 1.3.3                        

  - Add gene id to rownames to heatmap

                        Changes in version 1.3.2                        

  - Fixed a bug in prepare_3parts_genomic_features
      - Add messages to each function

                        Changes in version 1.3.1                        

  - Updated dependency on R >= 4.4.0 and genomation >= 1.36.0

                       Changes in version 1.1.10                        

  - Handle NCBI style of seqlevels (seqname)

                        Changes in version 1.1.9                        

  - Fixed a bug in plot_region

                        Changes in version 1.1.8                        

NEW FEATURES

  - Add handling of .gz files for bed and bedGraph format.
      - Add input filter for chromosomes. Only specified chromosomes
        will be included in visualization and analysis.

                        Changes in version 1.1.7                        

NEW FEATURES

  - Add handle_bedGraph to enable data input of bedGraph format

                        Changes in version 1.1.6                        

  - Merged a pull request from Hervé Pagès notifications@github.com

                        Changes in version 1.1.5                        

  - Added a function to obtain chromosome info from cached data in the
    'circlize' package to produce a Seqinfo object, which is applied to
    all GRanges and TxDB object
      - Added another function to generate a customized TxDb object from
        a genome annotation (GTF or GFF) file.

                        Changes in version 1.1.4                        

Change chromosome size information source from UCSC web service to
cached data in the 'circlize' package, to avoid internet connection
issues and web service issues.

                        Changes in version 1.1.3                        

Increase font size for axis labels, align profile with heatmap

                        Changes in version 1.1.1                        

Removed some suggests in DESCRIPTION to reduce installation time and
size

BUG FIXES

Fixed misalignment between profiles and heatmaps

                        Changes in version 1.0.0                        

Officially released on Bioconductor

                       Changes in version 0.99.15                       

NEW FEATURES

None

SIGNIFICANT CHANGES

  - Provide link to all external and internal data in manual
      - Add examples to all plot functions

BUG FIXES

None

                       Changes in version 0.99.14                       

NEW FEATURES

None

SIGNIFICANT CHANGES

  - Make txdb available in /inst/data to avoid repetitive generation of
    it in examples
      - Store gf5_meta and gf5_genomic in /data so that they can be
        loaded by calling data()
      - Create /R/data.R for data documentations

BUG FIXES

None

                       Changes in version 0.99.13                       

NEW FEATURES

None

SIGNIFICANT CHANGES

  - Add 'title' to draw_combo_plot function arguments.

BUG FIXES

  - Fixed a bug in plot_peak_annotation, such that txdb$user_genome is
    treated as a vector of strings rather than a single string

                       Changes in version 0.99.12                       

NEW FEATURES

  - Add PCA plot in plot_bam_correlation.
      - The function plot_5parts_metagene can generate profile plots for
        both 5 parts (Promoter, 5'UTR, CDS, 3'UTR, TTS) and 3 parts
        (Promoter, Gene, TTS) metagene.

SIGNIFICANT CHANGES

  - The function plot_3parts_metagene is removed.
      - Add setImportParams function to provide default import
        parameters.
      - Add saveRds option to import parameters to control saving of
        imported data, the default is FALSE.
      - Add data type and missing file checking for function arguments

BUG FIXES

None