nico_tutorial
A package that performs cell type annotations on single cell resolution of spatial transcriptomics data, find the niche interactions and statistically enriched covariation of gene programs between interacting cell types from the neighborhood.
spatialvi
Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
SpotClean
R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data
SEraster
Spatial Experiments raster - a rasterization preprocessing framework for scalable spatial omics data analysis
enrichmap
EnrichMap: Spatially-informed enrichment analysis for functional interpretation of spatial transcriptomics.
https://github.com/christinehou11/humanhippocampus2024
Access to spatial HPC project data
visiumStitched
R package containing functions useful for stitching Visium capture areas. Related to the example human brain data described at http://research.libd.org/visiumStitched_brain/.
singleCellHaystack
Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).
BatchSVG
Identification of biased features from SVGs in spatial transcriptomics data
https://github.com/alexslemonade/scpca-nf
scpca-nf is the Nextflow workflow for processing Single-cell Pediatric Cancer Atlas Portal data
sdevelo
Multivariate stochastic modeling for transcriptional dynamics with cell-specific latent time using SDEvelo