Author: Junjie Xia

Address: Tay Lab The University of Chicago Chicago, IL 60637, USA

---

Single_cell_Prox_seq_data_analysis

This is a python-based computational pipeline including package scanpy, scvi, celltypist and Prox-seq custom script ProxseqClasses.

This repo will cover basic single cell analysis procedures including quality control, PCA, clustering, cell type annotation, and visiulization. Specifically, intergrated analysis of sc-RNA and sc-Proxseq data will be shown. Spatial data analysis which might cover PLA visiulization, cell type deconvolution, and cell-cell interaction will be presented further.

Details of ProxseqClasses.py

See https://github.com/tay-lab/Prox-seq_computation

For introduction to Prox-seq

visit https://github.com/tay-lab/Prox-seq

For scanpy package

see https://scanpy.readthedocs.io/en/stable/tutorials.html

For celltypist package

see https://github.com/Teichlab/celltypist

For scvi-tools package

see https://scvi-tools.org/

Data availability

The tutorial is based on pbmc dataset from 10x pipeline. PLA dataset is uploaded and RNA data can be found in NCBI’s Gene Expression Omnibus under accession numbers GSE149574.