David McGaughey

Calculate Velocity

1

As per https://bustools.github.io/BUS_notebooks_R/velocity.html

Is using DNTx is valuable? Not certain what the metric of "success" would be.

Do isoform-level tx calling with well data Inspiration: https://www.biorxiv.org/content/10.1101/2020.03.05.977991v3

Not sure, why, but PAX6 (http://exac.broadinstitute.org/gene/ENSG00000007372) is missing from the big table of z, pli, etc. scores (ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3.1/functional_gene_constraint)

`superheat::superheat(as.matrix(c(2,3,3)))` gives `Error in 1:ncol(X) : argument of length 0` while `superheat::superheat(cbind(as.matrix(c(2,3,3)), as.matrix(c(2,3,3)))` works just fine (as expected) This may be as simple as using `,drop=FALSE` for any `as.matrix` operations?

Feature request: color labels for categories

1

Like this: http://stackoverflow.com/questions/20901915/change-the-layout-of-heatmap-2-figure Ideally would be able to stack a few (3 or 4?) on top of each other. Options for col or row axis.

Performance issue: force.grid.hline = T

3

On my mega long (nearly 500 row) heatmap, forcing the hline with `force.grid.hline = T` increases the time to make a plot by a huge amount. I'm going from a...

geyser

37

Update the following URL to point to the GitHub repository of the package you wish to submit to _Bioconductor_ - Repository: https://github.com/davemcg/geyser Confirm the following by editing each check box...

Allow user to set cpu cores used

1

https://github.com/lkmklsmn/insct/blob/master/tnn/tnn.py#L39 As far as I can see `TNN` uses all available cores. Don't want the HPC people angry.

Some questions

6

1. Do you intend the PCA to be run on the counts data or transformed data? 2. I assume the PCA is run on the entire dataset (and not per...