NEWS

---

GenomicPlot 1.3.5

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

GenomicPlot 1.3.4

• Modify pseudo count for ratio matrix

GenomicPlot 1.3.3

• Add gene id to rownames to heatmap

GenomicPlot 1.3.2

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

GenomicPlot 1.3.1

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

GenomicPlot 1.1.10

• Handle NCBI style of seqlevels (seqname)

GenomicPlot 1.1.9

• Fixed a bug in plot_region

GenomicPlot 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.

GenomicPlot 1.1.7

NEW FEATURES

• Add handle_bedGraph to enable data input of bedGraph format

GenomicPlot 1.1.6

• Merged a pull request from Hervé Pagès [email protected]

GenomicPlot 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.

GenomicPlot 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.

GenomicPlot 1.1.3

Increase font size for axis labels, align profile with heatmap

GenomicPlot 1.1.1

Removed some suggests in DESCRIPTION to reduce installation time and size

BUG FIXES

Fixed misalignment between profiles and heatmaps

GenomicPlot 1.0.0

Officially released on Bioconductor

GenomicPlot 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

GenomicPlot 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

GenomicPlot 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

GenomicPlot 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