nmikolajewicz / scpipeline Goto Github PK

I recommend to combine scale.method and normalization_method_ps, as typically these are the same. Watch out for capitalization for consistent variable naming.
If you want, I can implement this change.
Furthermore, if you want, you can also add me as contributor ;)

Hi Nicholas,

Congratulation on your Nature publication. And tank you very much for your cool tool. I's very useful and might make scRNA-seq exploratory data analysis a lot more convenient...it's awesome :)

One point: along the way, finding and installing the required packages is not very convenient but.

Especially one required package for the
M06_GeneExpressionAssociation_public.Rmd
is not very obvious and easy to miss, as it is called in a "try" statement and doesn't raise an obvious "hey, please install library RISmed" flag but gives a rather cryptic error "Error in convertIdx" a bit further down.

-> solution: I would include it in the packages2load right at the top

Thanks again and looking forward to advance your cool pipeline! :)

Best,
Chris

Hi,
I am experiencing an error in Module 1 in the developer input chunk. I am receiving the error "Error in inputDataSpecification() : could not find function "inputDataSpecification" ". I have done some looking but can't find where this function is coming from. Can you please advise?
Thanks!

Hello Nicholas, I successfully installed the scPipeline. Thank you for developing such a useful tool!

But as a slow learner, I have a question to ask you. Despite reading the tutorials many times, I can't find a solution to resolve this problem
For example, I have 6 samples, 2 experimental groups, and each group has 3 Biological replicates;
So, I use 'M02_DataIntegration_public_v2.Rmd' integration all 6 samples in one '.Rdata'.
How should I do downstream analysis in two groups?
eg. In SeuratData(ifnb) I can use the command line ifnb.list <- SplitObject(ifnb, split.by = "stim") to divide into groups ('ctrl' and 'stim')

Yujie