/ilcdev

Primary LanguageJupyter Notebook

Code repository: Dynamic Regulation of Innate Lymphoid Cell Development During Ontogeny

This repository contains single-cell RNA-seq data processing codes of the paper Dynamic Regulation of Innate Lymphoid Cell Development During Ontogeny.

Contents:

  • Cell_Preprocessing_Steps
  • Cell_Integration
  • Cell_Dynamics
  • SCENIC_GRN
  • TSC_GRN
  • Cell_Identity_Mapping
  • DEG_Enrichment_and_CellMapping

Data Availablity:

The single-cell RNA sequencing data are available at GSA (https://ngdc.cncb.ac.cn/gsa/) with accession number CRA011319. Please feel free to contact us if you have any data analysis issues. (chensj16 ##AT## tsinghua ##DOT## org ##DOT## cn)

Prerequisite

The analyses were conducted under a R-4.1.1 python-3.7 environment. We used SeuratV4 and scanpy-1.8.2 to perform most scRNA-seq analyses. We suggested using docker for the SCENIC analysis.