Slide_seqv2

notebooks for loading Slide-seqV2 data and some associated analyses

publication: https://www.biorxiv.org/content/10.1101/2020.03.12.989806v1

data: https://singlecell.broadinstitute.org/single_cell/study/SCP815/sensitive-spatial-genome-wide-expression-profiling-at-cellular-resolution#study

List of notebooks:

SlideseqV2_basic_loading_plotting_submission: notebook for loading and plotting gene count data and total counts across array (for most users you will want to start here)

SlideseqV2_HDST_comparison_submission: loading and plotting Slide-seqV2 data versus HDST

SlideseqV2_visium_comparison_submission: loading and plotting Slide-seqV2 data versus visium

SlideseqV2_scVelo_eye_submission: loading precomputed UMAP along with Slide-seq array coordinates to plot latent time trajectories on Slide-seq data