NEWS.md
In reimandlab/ActiveDriverWGSR: A Driver Discovery Tool for Cancer Whole Genomes
ActiveDriverWGS 1.2.0
- Updated trinucleotide quantification in sequence and mutations. Trinucleotides on the inverse strand are now reverse complemented instead of complemented to match COSMIC signatures.
- More accurate and stable numeric estimates of expected mutations are provided as output instead of the Poisson-sampled estimates provided previously.
- The package now allows identification of genomic elements with significantly fewer mutations than expected, potentially reflecting negative selection of elements. This is enabled using an optional command line parameter detect_depleted_mutations. In the analysis depleted mutations, elements with enriched mutations are assigned non-significant P-values.
ActiveDriverWGS 1.1.2
- Bug fixed: datasets with very few unmutated elements (<10) previously failed to include these elements in results.
- New option: mitochondrial mutations can be analyzed (chrM).
ActiveDriverWGS 1.1.1
- Bug fixed: a rare set of very large elements with depletion of mutations would sometimes appear as enriched in mutations.
ActiveDriverWGS 1.1.0
Major Changes
- Alternative reference genomes for human (hg19, hg38) and mouse (mm9, mm10) are now supported. Default option is hg19.
- Full rewrite of ADWGS_rest for memory and speed efficiency.
- Improved handling on indels on boundaries of elements is now default. Removed parameter element_bias that controlled this behaviour earlier.
- README.rd and front page now include a simple example of running ActiveDriverWGS, and the vignette has been updated.
- Site IDs need to match element IDs. Example databases with PTM sites have been updated.
reimandlab/ActiveDriverWGSR documentation built on Feb. 26, 2024, 6:14 p.m.
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
ActiveDriverWGS 1.2.0
- Updated trinucleotide quantification in sequence and mutations. Trinucleotides on the inverse strand are now reverse complemented instead of complemented to match COSMIC signatures.
- More accurate and stable numeric estimates of expected mutations are provided as output instead of the Poisson-sampled estimates provided previously.
- The package now allows identification of genomic elements with significantly fewer mutations than expected, potentially reflecting negative selection of elements. This is enabled using an optional command line parameter detect_depleted_mutations. In the analysis depleted mutations, elements with enriched mutations are assigned non-significant P-values.
ActiveDriverWGS 1.1.2
- Bug fixed: datasets with very few unmutated elements (<10) previously failed to include these elements in results.
- New option: mitochondrial mutations can be analyzed (chrM).
ActiveDriverWGS 1.1.1
- Bug fixed: a rare set of very large elements with depletion of mutations would sometimes appear as enriched in mutations.
ActiveDriverWGS 1.1.0
Major Changes
- Alternative reference genomes for human (hg19, hg38) and mouse (mm9, mm10) are now supported. Default option is hg19.
- Full rewrite of ADWGS_rest for memory and speed efficiency.
- Improved handling on indels on boundaries of elements is now default. Removed parameter element_bias that controlled this behaviour earlier.
- README.rd and front page now include a simple example of running ActiveDriverWGS, and the vignette has been updated.
- Site IDs need to match element IDs. Example databases with PTM sites have been updated.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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