Todd A. Johnson

icon indicating an email [email protected]

icon company RIKEN IMS icon location Yokohama, Japan icon location Previously, worked on GWAS and statistical analyses for understanding variation in human traits and diseases. Now, working on cancer genome analyses.

Results 3 issues of Todd A. Johnson

Link to MCR does not work; here is a functioning link

The link to the MCR in the MutSig2CV README (and therefore this site) does not work, but the one that is in the reference file does work: http://www.mathworks.com/supportfiles/MCR_Runtime/R2013a/MCR_R2013a_glnxa64_installer.zip

SigProfilerMatrixGenerator: SciPy version 1.12.0 removed binom_test, so matrix generation run crashes

7 comment

I just updated the SigProfiler packages, and the update installed the latest SciPy 1.12.0. When running SigProfilerMatrixGenerator, it eventually crashed because the SciPy stats function binom_test, which was previously deprecated...

SigProfilerMatrixGenerator 1.2.26 is still broken: binomtest does not take a parameter "x"

1 comment

I just installed and ran SigProfilerMatrixGenerator 1.2.26, and it fails with an error that binomtest does not take a parameter _x_. The points in MutationMatrixGenerator.py all use binomtest(x=. According to...