James Ashmore

Hi Geoff, Thanks for the super fast reply! > Hi James, We used the log-normalized matrix for the OT computations. The truncated expression matrix was used in the regulatory regressions....

> Out of over 100 runs of 10x we threw out 1, which was very different than all our other samples. This was essentially a failed reaction. What about in...

> Wow, that's a lot of code! I think it would be a great addition. Only guideline is to open up a pull-request :) Great, I'll work on it this...

Hi @ivagljiva Thank you so much for the detailed response. I believe that has cleared up my confusion. Best, James

Hello @IanCodes Would you mind re-running the pipeline with the following configuration: min_samps_gene_expr: 0 min_gene_expr: 0 min_samps_feature_expr: 0 min_feature_expr: 0 min_samps_feature_prop: 0 min_feature_prop: 0 These parameters should effectively stop any...

> @SergioManzano10 I haven't had a response. I will use the standalone tool for the time being. Apologies for the lack of progress on this issue. Is it possible to...

> @jma1991 I have an urgent deadline this week and a conference next week. When I get back i'll look into sourcing the files to you. I had to delete...

> EDIT: I was easily able to get the files again, so if you can let me have contact details I can share them this week. Thanks. That's great, please...

Hello @adomingues I agree, using the same column names would be great - we'll look into this for either the next major/minor release. Thanks

Hello @paolo-kunderfranco Please could you send the input files which are passed to the run_stage.R script where the error occurs. With the input files, we can run the script by...