Chantriolnt Andreas Kapourani

icon indicating a website link https://andreaskapou.github.io/ icon indicating an email [email protected]

icon company University of Edinburgh icon location Edinburgh, UK icon location Post-doctoral fellow @EdinburghUni, @VallejosGroup and Neil Henderson. Machine learning and statistical modelling of single-cell genomics.

Results 5 comments of Chantriolnt Andreas Kapourani

Is dims.use actually working in RunHarmony?

Hi, not a developer of the package, but indeed there is an issue, which I highlighted in issue #151 , the solution is add a single line `embedding

Apply scMET on sliding windows

Dear Ning, Regarding your question, here is the code used in the paper (for the Ecker2017 dataset) for: 1. Running scMET on each chromosome: https://github.com/andreaskapou/scMET-analysis/blob/master/ecker2017/all_cells/00_run/fit_scmet_window.R 2. Combining the estimates of...

Apply scMET on sliding windows

Dear Ning, Yes, the way we did the analysis (line https://github.com/andreaskapou/scMET-analysis/blob/cd8700dc15e6eff590eafe0864ba17b94cb4ad23/ecker2017/all_cells/01_hvf/hvf_window.Rmd#L100) is to combine the output HVFs for each chromosome and then sort by (residual) overdispersion to extract the top...

How can I apply scMET on real data? And does it do imputation?

Hi, It's a shame you couldn't use Melissa for your analysis. The main difference is that scMET is not neither a clustering nor an imputation tool. Actually scMET can be...

create_region_object keeps running without an error

Hi, This is strange, this function should run relatively fast. Could you please share your output and commands here or directly via email ([email protected]) and I can have a look?...