Robert Amezquita

circos-like feature

1

I was looking at some code for the circlize package (produces circos-like graphics) and found the inputs to be very amenable for ggraph input - not sure if there's a...

When printing out the table 'two_players', in the subsequent text is a reference to column 'eb_estimate' however this is not printed. Could remove 'playerID' column from data or do a...

Last part of this section, the calculated cumulative/mean PEP is at odds with the writing (5.46% vs 4.43% respectively)

Additional Labels for Immgen Data

9

Proposing an additional layer of annotations for the T cell population. Splitting on CD4 vs CD8 would be first and foremost (looks like its already mostly doable by grepping on...

Porting to Safari

1

Any chance this extension could be ported to safari now that the Big Sur update has made it easier to port Chrome extensions to Safari?

`show.velocity.on.embedding.cor` calculations expensive - separate function?

8

When testing different visual parameters, it is pretty expensive to continually recalculate the delta projects, sqrt knn, transition probs, and such. Is there a way to save the results of...

Pass `colData(sce)` to enable facetting (feature request)

4

Feature request: would be super handy to pass along the cell-level metadata (`colData(sce)`) to enable facetting.

M-a / M-e : jump sentences (code chunks)

1

Wondering if there is an omission here that could be added in a future update - I use the `M-a`/`M-e` motion controls a lot to jump to the beginning/end of...

Bioconductor submission?

5

I saw some tags relating to bioc-check, and just wanted to check in on the status of Cellassign being submitted to BIoconductor. Thanks!

ATAC-seq/DNase-seq Analysis

13

Is there a way to run PePr without specifying input files, as is the case for analyzing ATAC-seq/DNase-seq data?