├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── LICENSE.md ├── NAMESPACE ├── R ├── class.R ├── demo.R ├── methods.R ├── plot.R ├── rev_gene.R ├── sysdata.R └── utils.R ├── README.md ├── SpaTalk.Rproj ├── data ├── geneinfo.rda ├── lrpairs.rda └── pathways.rda ├── img ├── SpaTalk.png ├── cor_heatmap.png ├── plot_cci_lrpairs.png ├── plot_cci_lrpairs_num.png ├── plot_lr_path.png ├── plot_lrpair.png ├── plot_lrpair_vln.png ├── plot_path2gene.png ├── st_celltype.png ├── st_celltype_all.png ├── st_celltype_density.png ├── st_celltype_percent.png ├── st_celltype_raster.png ├── st_gene_cell.png ├── st_gene_spot.png └── st_pie.png ├── inst ├── CITATION └── extdata │ ├── starmap_data.rda │ └── starmap_meta.rda ├── man ├── SpaTalk.Rd ├── createSpaTalk.Rd ├── dec_cci.Rd ├── dec_cci_all.Rd ├── dec_celltype.Rd ├── demo_dec_result.Rd ├── demo_geneinfo.Rd ├── demo_lrpairs.Rd ├── demo_pathways.Rd ├── demo_sc_data.Rd ├── demo_st_data.Rd ├── demo_st_meta.Rd ├── demo_st_sc_data.Rd ├── demo_st_sc_meta.Rd ├── find_lr_path.Rd ├── geneinfo.Rd ├── generate_spot.Rd ├── get_lr_path.Rd ├── lrpairs.Rd ├── pathways.Rd ├── plot_ccdist.Rd ├── plot_cci_lrpairs.Rd ├── plot_lr_path.Rd ├── plot_lrpair.Rd ├── plot_lrpair_vln.Rd ├── plot_path2gene.Rd ├── plot_st_celltype.Rd ├── plot_st_celltype_all.Rd ├── plot_st_celltype_density.Rd ├── plot_st_celltype_percent.Rd ├── plot_st_cor_heatmap.Rd ├── plot_st_gene.Rd ├── plot_st_pie.Rd ├── plot_st_pie_generate.Rd ├── rev_gene.Rd ├── set_expected_cell.Rd └── show-SpaTalk-method.Rd ├── script ├── cellcall.R ├── cellchat.R ├── cellphonedb.sh ├── cytotalk.R ├── giotto.R ├── max_hop.R ├── nichenetr.R ├── spaotsc.sh └── starmap.R └── vignettes ├── .gitignore └── SpaTalk.pdf /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/.gitignore -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /LICENSE.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/LICENSE.md -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/NAMESPACE -------------------------------------------------------------------------------- /R/class.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/R/class.R -------------------------------------------------------------------------------- /R/demo.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/R/demo.R -------------------------------------------------------------------------------- /R/methods.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/R/methods.R -------------------------------------------------------------------------------- /R/plot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/R/plot.R -------------------------------------------------------------------------------- /R/rev_gene.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/R/rev_gene.R -------------------------------------------------------------------------------- /R/sysdata.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/R/sysdata.R -------------------------------------------------------------------------------- /R/utils.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/R/utils.R -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/README.md -------------------------------------------------------------------------------- /SpaTalk.Rproj: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/SpaTalk.Rproj -------------------------------------------------------------------------------- /data/geneinfo.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/data/geneinfo.rda -------------------------------------------------------------------------------- /data/lrpairs.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/data/lrpairs.rda -------------------------------------------------------------------------------- /data/pathways.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/data/pathways.rda -------------------------------------------------------------------------------- /img/SpaTalk.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/img/SpaTalk.png -------------------------------------------------------------------------------- /img/cor_heatmap.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/img/cor_heatmap.png -------------------------------------------------------------------------------- /img/plot_cci_lrpairs.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/img/plot_cci_lrpairs.png -------------------------------------------------------------------------------- /img/plot_cci_lrpairs_num.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/img/plot_cci_lrpairs_num.png -------------------------------------------------------------------------------- /img/plot_lr_path.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/img/plot_lr_path.png -------------------------------------------------------------------------------- /img/plot_lrpair.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/img/plot_lrpair.png -------------------------------------------------------------------------------- /img/plot_lrpair_vln.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/img/plot_lrpair_vln.png -------------------------------------------------------------------------------- /img/plot_path2gene.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/img/plot_path2gene.png -------------------------------------------------------------------------------- /img/st_celltype.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/img/st_celltype.png -------------------------------------------------------------------------------- /img/st_celltype_all.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/img/st_celltype_all.png -------------------------------------------------------------------------------- /img/st_celltype_density.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/img/st_celltype_density.png -------------------------------------------------------------------------------- /img/st_celltype_percent.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/img/st_celltype_percent.png -------------------------------------------------------------------------------- /img/st_celltype_raster.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/img/st_celltype_raster.png -------------------------------------------------------------------------------- /img/st_gene_cell.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/img/st_gene_cell.png -------------------------------------------------------------------------------- /img/st_gene_spot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/img/st_gene_spot.png -------------------------------------------------------------------------------- /img/st_pie.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/img/st_pie.png -------------------------------------------------------------------------------- /inst/CITATION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/inst/CITATION -------------------------------------------------------------------------------- /inst/extdata/starmap_data.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/inst/extdata/starmap_data.rda -------------------------------------------------------------------------------- /inst/extdata/starmap_meta.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/inst/extdata/starmap_meta.rda -------------------------------------------------------------------------------- /man/SpaTalk.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/man/SpaTalk.Rd -------------------------------------------------------------------------------- /man/createSpaTalk.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/man/createSpaTalk.Rd -------------------------------------------------------------------------------- /man/dec_cci.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/man/dec_cci.Rd -------------------------------------------------------------------------------- /man/dec_cci_all.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/man/dec_cci_all.Rd -------------------------------------------------------------------------------- /man/dec_celltype.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/man/dec_celltype.Rd -------------------------------------------------------------------------------- /man/demo_dec_result.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/man/demo_dec_result.Rd -------------------------------------------------------------------------------- /man/demo_geneinfo.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/man/demo_geneinfo.Rd -------------------------------------------------------------------------------- /man/demo_lrpairs.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/man/demo_lrpairs.Rd -------------------------------------------------------------------------------- /man/demo_pathways.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/man/demo_pathways.Rd -------------------------------------------------------------------------------- /man/demo_sc_data.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/man/demo_sc_data.Rd -------------------------------------------------------------------------------- /man/demo_st_data.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/man/demo_st_data.Rd -------------------------------------------------------------------------------- /man/demo_st_meta.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/man/demo_st_meta.Rd -------------------------------------------------------------------------------- /man/demo_st_sc_data.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/man/demo_st_sc_data.Rd -------------------------------------------------------------------------------- /man/demo_st_sc_meta.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/man/demo_st_sc_meta.Rd -------------------------------------------------------------------------------- /man/find_lr_path.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/man/find_lr_path.Rd -------------------------------------------------------------------------------- /man/geneinfo.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/man/geneinfo.Rd -------------------------------------------------------------------------------- /man/generate_spot.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/man/generate_spot.Rd -------------------------------------------------------------------------------- /man/get_lr_path.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/man/get_lr_path.Rd -------------------------------------------------------------------------------- /man/lrpairs.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/man/lrpairs.Rd -------------------------------------------------------------------------------- /man/pathways.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/man/pathways.Rd -------------------------------------------------------------------------------- /man/plot_ccdist.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/man/plot_ccdist.Rd -------------------------------------------------------------------------------- /man/plot_cci_lrpairs.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/man/plot_cci_lrpairs.Rd -------------------------------------------------------------------------------- /man/plot_lr_path.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/man/plot_lr_path.Rd -------------------------------------------------------------------------------- /man/plot_lrpair.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/man/plot_lrpair.Rd -------------------------------------------------------------------------------- /man/plot_lrpair_vln.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/man/plot_lrpair_vln.Rd -------------------------------------------------------------------------------- /man/plot_path2gene.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/man/plot_path2gene.Rd -------------------------------------------------------------------------------- /man/plot_st_celltype.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/man/plot_st_celltype.Rd -------------------------------------------------------------------------------- /man/plot_st_celltype_all.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/man/plot_st_celltype_all.Rd -------------------------------------------------------------------------------- /man/plot_st_celltype_density.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/man/plot_st_celltype_density.Rd -------------------------------------------------------------------------------- /man/plot_st_celltype_percent.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/man/plot_st_celltype_percent.Rd -------------------------------------------------------------------------------- /man/plot_st_cor_heatmap.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/man/plot_st_cor_heatmap.Rd -------------------------------------------------------------------------------- /man/plot_st_gene.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/man/plot_st_gene.Rd -------------------------------------------------------------------------------- /man/plot_st_pie.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/man/plot_st_pie.Rd -------------------------------------------------------------------------------- /man/plot_st_pie_generate.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/man/plot_st_pie_generate.Rd -------------------------------------------------------------------------------- /man/rev_gene.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/man/rev_gene.Rd -------------------------------------------------------------------------------- /man/set_expected_cell.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/man/set_expected_cell.Rd -------------------------------------------------------------------------------- /man/show-SpaTalk-method.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/man/show-SpaTalk-method.Rd -------------------------------------------------------------------------------- /script/cellcall.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/script/cellcall.R -------------------------------------------------------------------------------- /script/cellchat.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/script/cellchat.R -------------------------------------------------------------------------------- /script/cellphonedb.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/script/cellphonedb.sh -------------------------------------------------------------------------------- /script/cytotalk.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/script/cytotalk.R -------------------------------------------------------------------------------- /script/giotto.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/script/giotto.R -------------------------------------------------------------------------------- /script/max_hop.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/script/max_hop.R -------------------------------------------------------------------------------- /script/nichenetr.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/script/nichenetr.R -------------------------------------------------------------------------------- /script/spaotsc.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/script/spaotsc.sh -------------------------------------------------------------------------------- /script/starmap.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/script/starmap.R -------------------------------------------------------------------------------- /vignettes/.gitignore: -------------------------------------------------------------------------------- 1 | *.Rmd 2 | -------------------------------------------------------------------------------- /vignettes/SpaTalk.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZJUFanLab/SpaTalk/HEAD/vignettes/SpaTalk.pdf --------------------------------------------------------------------------------