Release 1.1.3 "Paris"

Bug Fixing

Full Changelog: 1.1.2...1.1.3

Assets 2

12 Aug 13:26

ProCESS 1.1.2

Release 1.1.2 "Sant'Anna di Stazzema"

Bug Fixing

Fixed an issue in annotate_forest() that labels any passenger CNA (Issue #143)
Added rvest among the package imports
Improved Simulating Mutations vignette

Full Changelog: 1.1.1...1.1.2

Assets 2

08 Aug 16:21

ProCESS 1.1.1

Bug Fixing

fixed a wrong warning message suggesting to decreaseMutationEngine's parameter max_repetition_storage, instead of increasing it.
fixed a wrong warning message saying that TissueSimulation$get_sample_forest() is deprecated. Actually, TissueSimulation$get_samples_forest() is deprecated.
replaced "samples forest" with "sample forest" in documentation and site figures.
fixed documentation typos and issues for TissueRectangle$lower_corner, TissueSimulation$search_sample, and SampleForest$get_subforest_for.
math rendering is now performed by KaTeX.

Full Changelog: 1.1.0...1.1.1

Assets 2

14 Jul 11:53

ProCESS 1.1.0

New features

New driver mutations
New passenger CNA
Exposures are now probability distributions for signatures. The number of passenger mutations are evaluated from a Poisson distribution whose parameter is genome size mutiplied by mutation rate. The mutations are associated to the active exposure's signatures according to a multi-modal distribution whose probabilities are defined by the exposure itself.
Simulated reads are now labelled by cell id code.
API refactoring (the old API is still available, but it raises warnings):
- SpatialSimulation is now TissueSimulation
- MutationEngine$get_samples_forest() is now MutationEngine$get_sample_forest()
- SamplesForest is now SampleForest.
Every driver mutation is now validated on the reference genome. If the reference reported in the mutation differs from the reference genome, then the execution is stopped.
PhylogeneticForest$get_driver_mutations() now reports driver codes when available
If the same driver mutation is added more than once in the same call to MutationEngine$add_mutant(), then the execution is stopped.
If a known driver mutation is added as a driver in a tumour whose type has been specified in MutationEngine() and the specified tumour type is not among those for which the mutation is known to be a driver, then MutationEngine$add_mutant() raises a warning.
A warning is raised if a context type or a repetition pattern are not available for passenger mutation placing.