Lucas Graybuck

Recommended by Fahimeh: We should build a workflow showing which functions are used for each step of analysis, analogous to our supplementary figure.

Currently, findVG both computes statistics for variable genes and can optionally output plots to a file as a side effect. Instead, we should split this up to 3 functions: 1...

We need to have a mode for clustering that doesn't write files to the users' machine. This is not normal behavior for most functions. The outputs aren't very large, so...

Running iterative clustering dumps a lot of text to the console. We should be able to toggle or adjust this behavior throughout scrattch.hicat.

Hi Monti Lab team, Thanks for assembling this great toolkit! It's really streamlining my DEG pathway analysis. I've run into a bug around retrieving the MSigDB C7 (Immunologic Signatures) gene...

MouseLight reconstructions

5

Add functions to draw MouseLight reconstructions into the 3D brain plots. These can be downloaded in SWC format: http://research.mssm.edu/cnic/swc.html

Paritioning/Slicing 3D CCF objects

1

Can we find a way to split CCF meshes into custom sub-regions? For example, divide PAG into dmPAG/dlPAG, etc as shown here: https://www.researchgate.net/figure/Circuitry-of-the-periaqueductal-gray-area-PAG-associated-with-defensive-behavior-In_fig5_263236478 Resources: https://github.com/zarquon42b/mesheR https://cran.r-project.org/web/packages/Rvcg/ http://zarquon42b.github.io/

Dashes in gene names cause missing gene errors.

If group_violins_plot has a aes(group =), can we get proper violin separation even for groups with identical color values?

If a group is missing (e.g. only group_id 1 and group_id 3 are present) but groups 1:3 are selected for plotting in a group heatmap plot, there is a blank...