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

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

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

Bugfixes:
* Fix running of the code examples.

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

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

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
  Sample can be hierarchically clustered.

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

Fourth preparation release for Bioconductor 3.5.

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

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

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)
=====================================================

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)
=====================================================

Second preparation release for Bioconductor 3.5.


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

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)
=====================================================

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