Spatiotemporal modeling of spatial transcriptomics
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Updated
Jul 7, 2024 - Python
Spatiotemporal modeling of spatial transcriptomics
Spatial dissimilarity analysis in single cells
Technology-invariant pipeline for spatial omics analysis (Xenium / MERSCOPE / CosMx / PhenoCycler / MACSima / Hyperion) that scales to millions of cells
Python package to perform enrichment analysis from omics data.
MIXER: An integrative algorithm for identifying co-expressed and cofunctional genes in multimodal transcriptomic sequencing data
Code for the spatialLIBD R/Bioconductor package and shiny app
HEST: Bringing Spatial Transcriptomics and Histopathology together
R package containing functions useful for stitching Visium capture areas. Related to https://github.com/LieberInstitute/LS_visiumStitched
Associated code to the manuscript "Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using high definition spatial profiling"
Scatterbar - an alternative data visualization for proportional data across many spatially resolved coordinates
general repo that holds all analysis and figures for the thymus spatial atlas by Yayon, Kedlian, Boehme, Radtke and many more!
scpca-nf is the Nextflow workflow for processing Single-cell Pediatric Cancer Atlas Portal data
Spatial Single Cell Analysis in Python
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.
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.
This repository will continuously collect annotated spatial transcriptomic datasets. 本仓库将持续收集空间转录组数据集
R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
Spatial Deconvolution method with Platform Effect Removal
Analysis of Array-seq ST Datasets
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