Stephen Williams

I work in the biomedical sciences and many times we'd like to view the same output across multiple condition so viewing everything on the same scale is important to make...

Stephen/spaceranger2.0

2

This PR updates scanpy to accommodate the latest changes made in spaceranger 2.0 which will break the released version of scanpy. Will provide backwards compatibility to pre 2.0 releases.

Question: Where is register(MulticoreParam(8)) being used

1

I was wondering where in chromVAR parallel processing was being used. In the vignette it is stated to set ``` library(BiocParallel) register(MulticoreParam(8)) ``` but in digging through the code I...

I have a shiny app where the user enters a sample ID and I'm checking whether it's correct or not. I'd like to provide feedback as to whether the ID...

feat: visium hd cell segmentation example

4

Provides working example of using Visium HD cell segmentations available with Spaceranger 4.0+. Goes from loading data, to simple QC, to clustering and visualization.

feature: updates for cellranger 9.0

5

This PR adds support for cellranger 9.0 which performs automatic cell type annotation. Creates a simple loading function similar to `Load10x_spatial` for 10x single cell data which will also put...

Feature: Updates for Space Ranger 4.0

14

Updates include helpers and readers for Space Ranger cell segmentation. Integrates 10x cell segmentations of visium HD data into the Seurat object. Issues - [ ] Converting the SF object...