Methods paper available Open Access

Our methods paper describing the denovolyzeR package is now freely available on PubMed Central.

New release and critical bug fix

A critical bug has recently been identified in the previous version of denovolyzeR. When analysing the frequency of de novo variants for individual genes (either using denovolyzeByGene, or denovolyze(...,groupBy="gene")), the output column labels may not have matched the data content under certain circumstances. This occurred if the default parameters were overridden by the user using the includeClasses argument.

This bug has now been fixed in release 0.2.0.

Other changes:

  • The output format has changed so that all data is returned in columns within the output data.frame. Previously either "gene" or "class" was returned in the rownames of the output data structure.
  • One of the package dependencies has been updated (reshape to reshape2).

New release

A new version (0.1.1) was released on 2016-06-18, to ensure compatibility with a new version of dplyr (0.5.0, published 2016-06-24).

Changes are backwards compatible, with features unchanged.

There may be trouble ahead...

We have received fair warning that the the forthcoming release of dplyr (due for CRAN submission on April 25) may not be backwards compatible with denovolyzeR. I will investigate this ASAP. Until this is addressed users may need to keep an installation of dplyr 0.4.3 on their system in order to run denovolyzeR.

de novo mutations in Congenital Heart Disease with neurodevelopmental and other birth defects

Our latest paper, using denovolyzeR to analyse de novo mutations in congenital heart disease came out today in Science.