MutationalPatterns v1.7.3 (Release date: 2018-10-19)
=====================================================

Changes:

* Update Francis's e-mail address.


MutationalPatterns v1.4.3 (Release date: 2018-03-16)
=====================================================

Changes:

* Bugfixes:
  + Fix colors in plot_rainfall so that missing substitutions don't shift colors.
  + Return a ggplot object from plot_enrichment_depletion.

* Other:
  + Move gridExtra to suggested packages because it isn't
    used in the code.  The vignette does use it to show
    how plots can be combined into a single figure.


MutationalPatterns v1.4.2 (Release date: 2017-12-19)
=====================================================

Changes:

* Improvements.
  + Improve error handling with parallel functions.

* Bugfixes:
  + Fix bug related to generic function overlap between NMF and DelayedArray.
  + Up the cowplot dependency to fix empty plots bug.


MutationalPatterns v1.4.1 (Release date: 2017-11-13)
=====================================================

Changes:

* Improvements:
  + Avoid letting lines run off the paper in the PDF vignette.


MutationalPatterns v1.4.0 (Release date: 2017-10-30)
=====================================================

Changes:

* Bioconductor 3.6 release.


MutationalPatterns v1.3.2 (Release date: 2017-10-24)
=====================================================

Changes:

* Bugfixes:
  + Removed deprecated functions from previous release.
  + Improved examples in documentation.


MutationalPatterns v1.3.1 (Release date: 2017-10-24)
=====================================================

Changes:

* Bugfixes:
  + Fix running of the code examples.


MutationalPatterns v1.3.0 (Release date: 2017-10-22)
=====================================================

Changes:

* Bugfixes:
  + To determine the transcriptional strand of mutations in genes,
    all mutations that overlap with multiple genes were excluded.
    When these genes are on different strands, it can indeed not
    be determined whether a mutation is on the transcribed or
    untransribed strand. However, if these overlapping genes are all
    on the same strand, the transcriptional strand can be determined,
    but these were unneccesarily removed from the analysis.
    This bug is now fixed, and as a result more mutations are now
    included in the analysis.
    This bugfix influences the results of:
    'mut_strand' (previously 'strand_from_vcf') and 'mut_matrix_stranded'

* Renamed functions:
  + 'strand_from_vcf' to 'mut_strand'
  + 'mutation_types' to 'mut_type'
  + 'mutation_context' to 'mut_context'

* New features & parameter changes:
  + Replicative strand bias analyses
    - 'mut_strand' and 'mut_matrix_stranded' can now be executed in two modes:
      'transcription' (default) or 'replication'
    - All downstream analyses can be performed for both modes with
      'strand_occurrences', 'strand_bias_test' and 'plot_strand_bias'
  + Condensed plotting option for 'plot_96_profile' and 'plot_192_profile'
    condensed = F (default), or condensed = T
  + Sample can be hierarchically clustered.

* New functions:
  + 'plot_contribution_heatmap': to visualize the relative contribution of
    mutational signatures in a heatmap. Samples can be hierarchically clustered.
  + 'cos_sim': to calculate the cosine similarity between two vectors.
  + 'cos_sim_matrix': to calculate all pairwise similarities between mutational profiles
  + 'cluster_signatures': to hierarchically cluster signatures based on cosine similarity
  + 'plot_cosine_heatmap': to visualize pairwise cosine similarities between mutational profiles in a heatmap


MutationalPatterns v1.1.3 (Release date: 2017-04-20)
=====================================================

Changes:

* Fourth preparation release for Bioconductor 3.5.

* Bugfixes:
  + Add missing package to 'Suggest' field.


MutationalPatterns v1.1.3 (Release date: 2017-04-20)
=====================================================

Changes:

* Third preparation release for Bioconductor 3.5.

* Bugfixes:
  + Fix running of a unit test.
  + Fix another build problem for Windows.


MutationalPatterns v1.1.2 (Release date: 2017-04-18)
=====================================================

Changes:

* Third preparation release for Bioconductor 3.5.

* Bugfixes:
  + Properly read external data for tests.
  + Fix build problems on Windows.


MutationalPatterns v1.1.1 (Release date: 2017-04-12)
=====================================================

Changes:

* Second preparation release for Bioconductor 3.5.


MutationalPatterns v1.1.0 (Release date: 2017-04-06)
=====================================================

Changes:

* Preparations for Bioconductor release 3.5.

* Interface changes:
  + 'read_vcfs_as_granges':  The 'genome' parameter
    must now be the name of a BSgenome library, to prevent
    problems with seqlevels style.

    The function now accepts an optional 'group' parameter to
    use a subset of chromosomes.

    It also accepts  the new optional 'check_alleles'
    parameter to significantly speed up the reading of VCF files.

  + 'plot_contribution': This function now accepts an
    optional parameter 'palette' to specify custom colors.

* Performance updates:
  + Implement parallel execution in 'read_vcfs_as_granges',
    'mut_matrix' and 'mut_matrix_stranded'.

* Bugfixes:
  + Fix 'mut_type_occurences' to handle missing types.
  + Fix 'mut_matrix' and 'mut_matrix_stranded' to emit warnings
    when processing empty GRanges.
  + Fix inconsistencies in the README and the vignette.

* Other changes:
  + Various vignette updates.
  + Added unit tests for 'read_vcfs_as_granges', 'mut_matrix',
    and 'mut_matrix_stranded'.


MutationalPatterns v1.0.0 (Release date: 2016-10-19)
=====================================================

Changes:

* Bioconductor release 3.4.


MutationalPatterns v0.99.6 (Release date: 2016-10-14)
=====================================================

Changes:

* Renamed functions:
  + 'mut_type_occurences' to 'mut_type_occurrences',
  + 'strand_occurences' to 'strand_occurrences'.


MutationalPatterns v0.99.5 (Release date: 2016-10-06)
=====================================================

Changes:

* Added deprecation and defunct messages to functions that have
  changed since the v0.99.0.
* Various small vignette and reference manual updates.


MutationalPatterns v0.99.4 (Release date: 2016-10-05)
=====================================================

Changes:

* Internal package loading changes.
* Removed files that do not belong to the package.


MutationalPatterns v0.99.3 (Release date: 2016-09-28)
=====================================================

Changes:

* Renamed functions:
  + 'get_mut_context' to 'mutation_context',
  + 'get_type_context' to 'type_context',
  + 'get_muts' to 'mutations_from_vcf',
  + 'get_strand' to 'strand_from_vcf'.

* Added an explanation for the difference between SomaticSignatures
  and MutationalPatterns in the vignette.


MutationalPatterns v0.99.2 (Release date: 2016-09-23)
=====================================================

Changes:

* Renamed functions: 'vcf_to_granges' to 'read_vcfs_as_granges',
    'get_types' to 'mutation_types'.


MutationalPatterns v0.99.1 (Release date: 2016-09-13)
=====================================================

Changes:

* Renamed functions:
  + 'read_vcf' to 'vcf_to_granges'.

* Removed functions:
  + 'bed_to_granges',
  + 'estimate_rank',
  + 'rename_chrom'.

* Parameter changes:
  + 'plot_rainfall',
  + 'vcf_to_granges'.


MutationalPatterns v0.99.0 (Release date: 2016-09-12)
=====================================================

Changes:

* Package created