Samuel Marsh comments

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                                            Samuel Marsh

Can't exclude factors from louvainCluster

Hi Karl, Not member of dev team but have you tried the solution shown in in Liu et al., 2020 (Nature Protocols) (pg 3645). https://www.nature.com/articles/s41596-020-0391-8 _To remove these factors from...

online_iNMF error

Hi Chao, Sorry should have added in my original comment this is an all in memory dataset as it's reanalysis from large published dataset and the only files they provided...

online_iNMF error

Hi Chao, Yes, that is what I'm doing. That is how I know that when I filter with keep

Problem with package name change: load older liger object

Ya not sure either. If you do happen to have the other "liger" package installed then the objects will load and you can interact with them properly using rliger. But...

Problem with package name change: load older liger object

Ya I've done similar thing within R using packrat/renv packages. I mean one other solution is that user can download the old release from github directly where package is named...

Add `keep.meta` parameter to `ligerToSeurat`

Excellent! Thanks for the double check Paul!

Add `keep.meta` parameter to `ligerToSeurat`

Hi Welch Lab/LIGER team, Just wanted to ping on this PR and see if it could be merged soon? Easiest for reproducibility if it's part of package. Thanks! Sam

Add `keep.meta` parameter to `ligerToSeurat`

Closing this as devs have not commented in 2 years.

Add `keep.meta` parameter to `ligerToSeurat`

Hi @cgao90 yes sorry I was working on another PR to resubmit with this one too but then got sidetracked. I’ll re add and push this week. Thanks so much!!

Load .RDS files directly into environment `gcs_get_object`?

Hi Mark, Thanks for quick response. This must be what I'm not quite understanding because when I run: ``` obj