SCXA analysis workflow updates 2021

[pinin4fjords]

This is the work-in progress to implement some workflow updates recommended to us by Chichau, subject to successful evaluation.

Edit, September '21:

Following thorough evaluation, the following changes were implemented:

Base param set:

• Switch to filter based on counts only, > 1500
• Add mitochondrial threshold of 35%
• Switch marker genes to Wilcoxon method

Droplet experiments

• Add scaling step (required some wiring to do this but supply the un-scaled matrix to the marker genes step)
• Add Scrublet

For batched experiments

• Add batch to HVG step, alongside use of Harmony

SMART workflow: here. Droplet workflow: here .

[pinin4fjords]

Current changes ready to go, tested on droplet, plate, batched and unbatched

[pinin4fjords]

• Droplet pipeline available here
• Plate pipeline available here

[pinin4fjords]

Thanks @pcm32 !