Single-cell RNA-seq Analysis of Chicken

Analysis pipelines for the Chicken Single Cell Atlas 1. Introduction We present a comprehensive chicken single-cell atlas comprising 1.57 million cells across 36 tissues and 157 cell types. This resource reveals the evolutionary dynamics of avian cell types, particularly immune cells, and provides new insights into immune system evolution across amniotes. 2. Analysis pipeline This repository contains the analysis pipelines used in the Chicken Single Cell Atlas, including: CARD for spatial transcriptomics analysis CCA integration for data integration CellChat for cell–cell communication analysis Gene expression pattern analysis MAST-based differential expression analysis for single-cell data MetaNeighbor for cell-type similarity analysis Monocle and Slingshot for cell developmental trajectory inference SCENIC/GENIE3 for transcriptional regulatory network analysis Seurat-based single-cell analysis Spearman correlation analysis WGCNA for weighted gene co-expression network analysis 3. Citation Chicken Single Cell Atlas