Jack Humphrey comments

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                                            Jack Humphrey

Does Leafviz work on leafcutterMD result?

I've considered adding this as part of the standalone LeafViz app. @GarrettJenkinson do you have any visualisation code that we could include?

PSI and covariates

Hi Dalila, Great idea! For 2. I'll implement covariate PCAs for LeafViz.

PSI and covariates

thanks for that David. I think stringr should already be a listed dependency. The function set_rownames comes from **magrittr** so you'll need to add that if it isn't already.

PSI and covariates

that's now done. I've deployed the latest changes to https://leafcutter.shinyapps.io/leafviz/

PSI and covariates

script is here: https://github.com/davidaknowles/leafcutter/blob/psi_2019/scripts/leafcutter_quantify_psi.R

A bug in `refine_cluster()`?

Yang, should we merge this PR? #146

LeafViz not plots

Apologies for the delay, are you still having this issue? Can you confirm whether this was on an example RData file or a file you generated yourself?

pip leafcutter command line tools

@davidaknowles

Is installation still possible?

Hi all, I had to re-install Leafcutter today due to my HPC updating R. I used the following recipe and it succeeded. ``` conda create -n leafcutter conda activate leafcutter...