├── LICENSE ├── README.md ├── codes ├── 0-1.read10xCounts.R ├── 0-2.prefilter.R ├── 0-3.combine_sclibs.R ├── 1a-1.seurat_cluster.R ├── 1a-2.seurat_cluster_rm.R ├── 1b-1.scanpy_seurat2anndata.R ├── 1b-2.scanpy_cluster.py ├── 1b-3.scanpy_anndata2seurat.R ├── 2-1.subclus_findmarker.R ├── 2-2.subclus_marker_plot.Rmd └── 2-2.subclus_marker_plot.run.sh └── raw_data_download.md /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/meta-cancer/scPLC/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/meta-cancer/scPLC/HEAD/README.md -------------------------------------------------------------------------------- /codes/0-1.read10xCounts.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/meta-cancer/scPLC/HEAD/codes/0-1.read10xCounts.R -------------------------------------------------------------------------------- /codes/0-2.prefilter.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/meta-cancer/scPLC/HEAD/codes/0-2.prefilter.R -------------------------------------------------------------------------------- /codes/0-3.combine_sclibs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/meta-cancer/scPLC/HEAD/codes/0-3.combine_sclibs.R -------------------------------------------------------------------------------- /codes/1a-1.seurat_cluster.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/meta-cancer/scPLC/HEAD/codes/1a-1.seurat_cluster.R -------------------------------------------------------------------------------- /codes/1a-2.seurat_cluster_rm.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/meta-cancer/scPLC/HEAD/codes/1a-2.seurat_cluster_rm.R -------------------------------------------------------------------------------- /codes/1b-1.scanpy_seurat2anndata.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/meta-cancer/scPLC/HEAD/codes/1b-1.scanpy_seurat2anndata.R -------------------------------------------------------------------------------- /codes/1b-2.scanpy_cluster.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/meta-cancer/scPLC/HEAD/codes/1b-2.scanpy_cluster.py -------------------------------------------------------------------------------- /codes/1b-3.scanpy_anndata2seurat.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/meta-cancer/scPLC/HEAD/codes/1b-3.scanpy_anndata2seurat.R -------------------------------------------------------------------------------- /codes/2-1.subclus_findmarker.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/meta-cancer/scPLC/HEAD/codes/2-1.subclus_findmarker.R -------------------------------------------------------------------------------- /codes/2-2.subclus_marker_plot.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/meta-cancer/scPLC/HEAD/codes/2-2.subclus_marker_plot.Rmd -------------------------------------------------------------------------------- /codes/2-2.subclus_marker_plot.run.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/meta-cancer/scPLC/HEAD/codes/2-2.subclus_marker_plot.run.sh -------------------------------------------------------------------------------- /raw_data_download.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/meta-cancer/scPLC/HEAD/raw_data_download.md --------------------------------------------------------------------------------