Fixd critial install error in R dpendency "Runit""
minor bugfixes
Fixed a parsing problem regarding the Cosmic and CCLE. databases
Fixed a parsing problem regarding the Cosmic and CCLE. databases
Fixed yet another VCF file parsing error associated with the VariantAnnotation R package parser.
Uniquorn experienced an error when parsing the internal test vcf file on Windows systems.
Unzipped the tested vcf file since VarriantAnnotion parser failed to read zipped file in future R version 3.6
Removed dependency on data.table
Removed data.table import due to biocondcutor request
Updated BiocView
Minor bugfixes regarding the removal of CCLs
Minor bugfixes regarding the removal of CCLs and reference libraries
Minor modifications to comply with Bioconductor regulations
Some more minor bugfixes
Minor bugfixes
Modified the package to work with large scale RNA-seq and small scale panel-seq data
Please note that this might break custom libraries. In case of questions please contact the author
Added a script to parse vcf files in a non-parallelized fashion.
Fixed critical bug which disabled identifying CCLs in single-thread mode.
Fixed rather major bug that led to too high penalty scores.
Fixed minor bug that led to incorrect penalty score calculation.
The function that measures random background-noise matches and calculates a threshold above the background strength has been updated to be more strict.
the new default inclusion weight has been set to 0.5 to optimally fit the new probabilistic model of version 1.0.9.
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
Fixed the installation of the package
Optimized the way confidence scores are calculated to increase the sensitivity and specificity of the method
Adjusted default confidence score to optimal threshold
Fixed errors connected to adding CLs
Confidence score is the central threshold now
Default is 3.0
The score is the negative log e of the q-value
Fixed error in threshold calculation
Extended length of BED file mutations shown in the IGV
Further minor fixes to statistics
Minor fixes to statistics
Replaced the absolute and relative cutoff with a p an q-value based on a binomial distribution
Further update test suite
Update testing suite
Fixed error in unit tests
Added Unit test feature
Minor documentation bugfixes.
General bugfixing.
Minor bugfix concerning output of CL identifications.
Minor bugfix concerning data parsing of CellMiner data.
Fixed a bug that lead to incorrect calculation of CoSMIC CLP CL mutation weights.
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'
Fixed vigniette
Moved NEWS.Rd from 'Uniquorn' to 'Uniquorn/inst'
Fixed NEWS section
Fixed unit testing
Fixed the Vignette: replaced the github-dependent installation with the biocLite installation
Identify cancer cell lines
Show which cancer cell line are contained
Show which mutations are annotated for selected cancer cell lines
Show which mutaitons are overall included
Parse cancer cell line custom data -> add your own samples and identify these