Samuel Marsh

Problem with package name change: load older liger object

5

Hi Liger Team, Running into issue trying to load an object that was created with package when it was named liger and loading it into workspace where package is now...

Proper axis labels 2D Plots

1

Hi Liger Team, Just wanted to ping and see if there are plans to address the issues of #130 and #94. It would be really great to allow storing of...

Add `keep.meta` parameter to `ligerToSeurat`

6

Hi LIGER team, Just another quick PR. This PR would add additional parameter to the `seuratToLiger` function that allows for moving additional metadata information (besides nGene, nUMI, and dataset) to...

Hi Liger Team, Just curious what the rationale is for the default of `set.dr.lims = FALSE` in the `plotGene` function? Seems like it would be more logical to have it...

online_iNMF error

4

Hi All, Again finding the online branch really helpful in analysis of some very large datasets but got an error today I hope you can help with. As setup for...

Load .RDS files directly into environment `gcs_get_object`?

13

Hi, This might be naive question and I might be missing something but wondering if there is way to load file saved as a .RDS file from GCP bucket directly...

Cairo Dependency

9

Hi, Thanks for creation and dev of this package, it’s super useful!! This issue is actually a question regarding your thoughts on package dependencies, specifically the Cairo package. Unless I’m...

Add parallel support AddModuleScore

2

Hi Seurat Team, Just a PR based on discussion in previous PR request #6348 to add support for `AddModuleScore` parallel processing. My solution uses future/future.apply packages so no additional dependencies....

Hi LIGER team, It seems at glance that louvain cluster function utilizes some of the cpp backend from Seurat to run clustering but defaults the algorithm option in the call...

Move progress bars to cli framework

1

- [ ] Using `cli_progress_along()` mainly - [ ] Rewrite pblapply functions to match format needed - [ ] Remove old pblapply options - [ ] Remove pbapply dependency