A package that performs cell type annotations on single cell resolution of spatial transcriptomics data, find the niche interactions and covariation patterns between interacted cell types.

R package containing functions useful for stitching Visium capture areas. Related to https://github.com/LieberInstitute/LS_visiumStitched

CellContrast: Reconstructing Spatial Relationships in Single-Cell RNA Sequencing Data via Deep Contrastive Learning

Spatial Deconvolution method with Platform Effect Removal

Analysing single-cell and DSP data to test the effect of copper chelation with TEPA in Neuroblastoma mice

This Github repository holds data, Notebooks and results of running SDePER on both Simulated and Real datasets, and Notebooks for figure panels in manuscript, as well as the codes for running other cell type deconvolution methods.

Spatiotemporal modeling of spatial transcriptomics

scCellFie, inspired by the MATLAB-based CellFie tool, offers advanced analysis of metabolic functions on Python using single-cell and spatial transcriptomics. Efficient and user-friendly, it integrates with Scanpy to extend CellFie's capabilities, enabling in-depth single-cell and spatial metabolic task analysis.

Open-ST: profile and analyze tissue transcriptomes in 3D with high resolution in your lab

Code for the spatialLIBD R/Bioconductor package and shiny app

The pipeline to process Novaseq dataset, from fastq to nge.

Spatial dissimilarity analysis in single cells

scpca-nf is the Nextflow workflow for processing Single-cell Pediatric Cancer Atlas Portal data

Spatial Transcriptomics Quantification pipeline for 10x Visium and H&E-stained whole slide images

DANCE: a deep learning library and benchmark platform for single-cell analysis

HEST: Bringing Spatial Transcriptomics and Histopathology together

A Julia package for single cell and spatial data analysis

A Julia package for single cell and spatial data analysis

Spatially-aware quality control for spatial transcriptomics