Are Bioinformatics Results Too Good To Be True?

I came across an interesting paper by Ann Boulesteix where she discusses the problem of false positive results being reported in the bioinformatics literature. She highlights two underlying phenomena that lead to this issue – “fishing for significance” and “publication bias”. The former phenomenon is characterized by researchers identifying datasets on which their method works better […]

New Version of rpubchem

Version 1.4.3 of rpubchem is out on CRAN. There’s some minor code cleanups and also a new function called get.aid.by.cid which allows you to get assay ID’s based on whether they contain a compound (either as an active, inactive, discrepant or just tested). This uses PUG to perform the query, so can be a bit […]

Updated Versions of R Packages

New versions of several of my R packages are now available on CRAN. rcdk 2.9.6 goes along with rcdklibs 1.2.3. The latter now uses the most recent cdk-1.2.x branch from Github. The former fixes a number of bugs relating to descriptor calculations, saving molecules in SD format and setting/getting properties on molecules. Unfortunately, because the […]