Changes in version 2.1.4 (2018-10-10):
Bioconductor compliance
o Minor bugfixes regarding the removal of CCLs
Changes in version 2.1.3 (2018-10-03):
Bioconductor compliance
o Minor bugfixes regarding the removal of CCLs and reference libraries
Changes in version 1.99.3 (2018-01-03):
Bioconductor compliance
o Minor modifications to comply with Bioconductor regulations
Changes in version 1.99.2 (2018-20-02):
Added RNA-seq and panel-seq capability
o Some more minor bugfixes
Changes in version 1.99.1 (2018-12-02):
Added RNA-seq and panel-seq capability
o Minor bugfixes
Changes in version 1.99.0 (2018-15-01):
Added RNA-seq and panel-seq capability
o Modified the package to work with large scale RNA-seq and small
scale panel-seq data
o Please note that this might break custom libraries. In case of
questions please contact the author
Changes in version 1.4.2 (2017-15-05):
Added critical scripts
o Added a script to parse vcf files in a non-parallelized fashion.
Changes in version 1.4.1 (2017-12-05):
Fixed yet another penalty function bug
o Fixed critical bug which disabled identifying CCLs in single-thread
mode.
Changes in version 1.3.1 (2016-28-11):
Fixed yet another penalty function bug
o Fixed rather major bug that led to too high penalty scores.
Changes in version 1.1.3 (2016-28-11):
Fixed penalty function bug
o Fixed minor bug that led to incorrect penalty score calculation.
Changes in version 1.1.2 (2016-28-11):
Change of penalty function
o The function that measures random background-noise matches and
calculates a threshold above the background strength has been
updated to be more strict.
Changes in version 1.1.1 (2016-10-18):
Change of default inclusion threshold
o the new default inclusion weight has been set to 0.5 to optimally
fit the new probabilistic model of version 1.0.9.
Changes in version 1.0.9 (2016-10-11):
Re-engineering of probabilistic model
o The likelihood to observe a mutation/ variant in a query that
matches a reference CCL's variant has been changed. The likelihood
was 1 / #all variants in library and is now set to # number of
variants in reference CCL / #all variants in library
Changes in version 1.0.8 (2016-06-17):
Optimization confidence score
o Fixed the installation of the package
Changes in version 1.0.7 (2016-06-13):
Optimization confidence score
o Optimized the way confidence scores are calculated to increase the
sensitivity and specificity of the method
Changes in version 1.0.6 (2016-06-05):
Optimization of default confidence score
o Adjusted default confidence score to optimal threshold
Changes in version 1.0.5 (2016-05-30):
Minor Bugfixes
o Fixed errors connected to adding CLs
Changes in version 1.0.4 (2016-05-27):
Introduction of confidence score
o Confidence score is the central threshold now
o Default is 3.0
o The score is the negative log e of the q-value
Changes in version 1.0.3 (2016-05-18):
Changes to treshold calculation
o Fixed error in threshold calculation
Changes in version 1.0.1 (2016-05-09):
Minor update of BED files
o Extended length of BED file mutations shown in the IGV
Changes in version 0.99.16 (2016-05-04):
Further minor update of statistics module
o Further minor fixes to statistics
Changes in version 0.99.15 (2016-05-03):
Minor Update of statistics
o Minor fixes to statistics
Changes in version 0.99.14 (2016-05-03):
Major Update of statistics
o Replaced the absolute and relative cutoff with a p an q-value based
on a binomial distribution
Changes in version 0.99.13 (2016-04-08):
Fixed unit tests
o Further update test suite
Changes in version 0.99.12 (2016-04-08):
Fixed unit tests
o Update testing suite
Changes in version 0.99.11 (2016-04-01):
Fixed unit tests
o Fixed error in unit tests
Changes in version 0.99.10 (2016-03-30):
Added Unit tests
o Added Unit test feature
Changes in version 0.99.9 (2016-03-29):
Improved documentation
o Minor documentation bugfixes.
Changes in version 0.99.8 (2016-03-25):
Fixed Bug
o General bugfixing.
Changes in version 0.99.7 (2016-03-24):
Fixed Bug
o Minor bugfix concerning output of CL identifications.
Changes in version 0.99.6 (2016-03-23):
Fixed Bug
o Minor bugfix concerning data parsing of CellMiner data.
Changes in version 0.99.5 (2016-03-22):
Fixed Bug
o Fixed a bug that lead to incorrect calculation of CoSMIC CLP CL
mutation weights.
Changes in version 0.99.4 (2016-03-16):
Added features
o Minimum amount of matching mutations required for a positive
prediction between query and training sample can now be manually
adjusted in the 'identify_vcf_file' function using the parameter
'miminum_matching_mutations'
Changes in version 0.99.3 (2016-03-02):
Fixed bugs
o Fixed vigniette
Changes in version 0.99.2 (2016-03-02):
Fixed bugs
o Moved NEWS.Rd from 'Uniquorn' to 'Uniquorn/inst'
Changes in version 0.99.1 (2016-03-02):
Fixed bugs
o Fixed NEWS section
o Fixed unit testing
o Fixed the Vignette: replaced the github-dependent installation with
the biocLite installation
Changes in version 0.99.0 (2015-01-27):
New features
o Identify cancer cell lines
o Show which cancer cell line are contained
o Show which mutations are annotated for selected cancer cell lines
o Show which mutaitons are overall included
o Parse cancer cell line custom data -> add your own samples and
identify these