Skip to content

TheHumphreysLab/IRI_Xenium_Visium

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

18 Commits
 
 
 
 
 
 
 
 

Repository files navigation

IRI_Xenium_Visium

Multimodal spatial transcriptomic characterization of mouse kidney injury and repair

Reproduce

Figure Description Code
Fig 2 Xenium data preprocessing and visualization link
Fig 3 Xenium PT spatial trajectory analysis link
Fig 4 Xenium cell neighborhood analysis link
Fig 5 A,B Xenium Visium registration and alignment link
Fig 5 E,F Visium cell neighborhood functional characterization link
Fig 5 G TF activity inference link
Fig 6 A Xenium LR analysis link
Fig 6 C-H Visium cell-cell communication link
Supple Fig 1 Xenium and Visium QC link
Supple Fig 3 Xenium snRNA-seq integration link
Supple Fig 8 Pseudo-Visium analysis link
Supple Fig 10 Xenium imputation link
Supple Fig 16 Benchmark segmentation algorithm on Xenium link
Supple Fig 17 Benchmark spot deconvolution algorithm on Visium link

Package

The pySTIM provides a comprehensive computational pipeline for the integration and analysis of spatial transcriptomics data. This tool is designed to integrate tissue histology with both high-definition spatial transcriptomics (e.g., Xenium) and transcriptome-wide spatial transcriptomics (e.g., Visium).

Installation

Installation using pip:
pip install pySTIM

Import

import pySTIM as pst

Usage

About

No description, website, or topics provided.

Resources

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published

Languages