scRNAseq and BulkRNAseq scripts for "Structured wound angiogenesis instructs mesenchymal barrier compartments in the regenerating nerve" publication
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- Tomato_scRNAseq_full_ds.R [TdTomato scRNAseq full dataset (containing also some fibroblasts, pericites, and LEC cells) prepropressing.]
- Tomato_scRNAseq_EC_only_ds.R [Analysis and carachterization of EC cell only clusters, isolated from the TdTomato scRNAseq full dataset]
- Carr_reanalysis.R [Re-analysis of Carr et al. 2019 scRNAseq dataset. GSE120678]
- Toma_reanalysis.R [Re-analysis of Toma et al. 2020 dataset. GSE147285]
- Kalinski_reanalysis.R [Re-analysis of Kalinski et al. 2020 dataset. GSE153762]
- Toma_Carr_Kalinski_Bonanomi_alluvial.R [Alluvial plot of the relative abundance of EC subtypes in the intact nerve or at different days post injury.]
- Milich_EC_label_transfer_alluvial.R [Re-analysis of Milich et al. GSE162610 spinal cord injury dataset]
- Ydens_reanalysis.R [Re-analyisis of Ydens et al. 2020]
- Merge_EC_MACs_SCHW_MES_Carr.R [Cells from different tissues and datasets were merged and clustered]
- CellChat_EC_MACs_SCHW_MES_Carr.R [Cell-Cell communication analysis with CellChat. EC, FIBRO, MACS, SCHWANN]
- monocle_pseudotime.R [EC pseudotime analysis with monocle2]
- dendrogram.R [EC dendrogram representation]
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- bulkRNASeq_Cherry.R [DGE analysis of our 7DPI WT and KO Cherry EC samples]
- bulkRNASeq_Tomato.R [DGE analysis of our intact, 7 DPI, 14 DPI TdTomato EC samples]
- metadata_cherry_tomato.xlsx [sample metadatda for our Cherry and TdTomato EC samples ]
- bulkRNASeq_Tomato_Corada.R [DGE analysis of our intact, 7 DPI, 14 DPI TdTomato samples + Corada et al. 2019 embryo and Adult samples ]
- metadata_tomato_corada.xlsx [sample metadatda for our TdTomato samples and Corada et al. 2019 samples]
- EWCE.R [Expression Weighted Cell Type Enrichment analysis to check the distribution of DEGs among EC subtypes]
- Associate_celltype_with_gene_name.R [DEG gene annotation according to scRNAseq expression]