BisqueRNA Functions not available for usage

Question

BisqueRNA Functions not available for usage

Amandahsr opened this issue 5 years ago · 3 comments

Great tool for bulk tissue deconvolution, its a great package and estimates really well!

May I ask if some of the BisqueRNA functions will be made available for usage? e.g. GenerateSCReference and SemisupervisedTransformBulk functions

Or if these functions cannot be made available for usage, could I suggest adding an additional output from the ReferenceBasedMethod that returns the transformed bulk counts? This can help users to plot distributions of the transformed datasets and run statistical tests

Answer 1 · 2020-07-17T22:54:24.000Z

Hi @Amandahsr

Thanks for the feedback! Just pushed a commit that adds the GenerateSCReference to the exported functions and returns the transformed bulk in the transformed.bulk slot of the output of ReferenceBasedDecomposition. These changes will be live on CRAN/Bioconda within the next day or two. Let me know if you have any questions or other comments

Brandon

Answer 2 · 2020-07-21T19:53:24.000Z

Hi brandon, thanks for the additional functions! However, it doesn't seem like these commits are available yet in the BisqueRNA package in R.

Answer 3 · 2020-07-21T19:59:27.000Z

Hi, the latest commits are live on CRAN for all operating systems. The package should be at version 1.0.4. You can make sure you have the latest version by running install.packages("BisqueRNA") again. Let me know if there's any issues.

Thanks!