Ability to add matrices for multi-modal analysis

[connorrogerson]

Hi team,

With the advent of multi-model single-cell assays with 3 modes (and probably more in the future), it's becoming more commonplace to have to add multiple matrices into one object. Think multiome+perturb-seq, which would have a GEX matrix, an ATAC matrix, and then guide count matrix. Or TEA-seq, which is GEX, ATAC and ADT matrix. The current inability for ArchR to import extra matrices is going to force people to use Seurat, in which you can easily add a third matrix. Some comments in the discussion are already hinting at this so I hope there are some conversations in the dev team as ArchR is by far my favourite tool.

[rcorces]

Hi Connor. I havent been very active on the GitHub these days but I figured it would be worth responding to this one. You are spot on - multi-modal support is really important these days. We are working on a new tool that is meant to be an "ArchR 2.0" with a different backend but all of the same types of functionalities that people like about ArchR. We dont have a timeline, but it is in the works and it will include the type of arbitrary multi-modal support you are talking about.

[connorrogerson]

Appreciate the reply! Looking forward to ArchR 2.0 soon... if you need any beta-testers let me know ;)