Update all analyses

analysis/scanpy-seurat-concordance.Rmd

@@ -38,7 +38,7 @@ seurat_wilcox <- readRDS(
 )
 
 scran_t_any <- readRDS(
-  here::here("results", "real_data", "pbmc3k-scran_t_any.rds")
+  here::here("results", "real_data", "pbmc3k-scran_findMarkers_t_any.rds")
 )
 ```
 

analysis/scran-any-case-study.Rmd

@@ -18,15 +18,15 @@ library(purrr)
 ```{r}
 pbmc3k <- readRDS(here::here("data", "real_data", "pbmc3k.rds"))
 pbmc3k_scran_t_any <- readRDS(
-  here::here("results", "real_data", "pbmc3k-scran_t_any.rds")
+  here::here("results", "real_data", "pbmc3k-scran_findMarkers_t_any.rds")
 )
 
 pbmc3k_scran_binom_any <- readRDS(
-  here::here("results", "real_data", "pbmc3k-scran_binom_any.rds")
+  here::here("results", "real_data", "pbmc3k-scran_findMarkers_binom_any.rds")
 )
 
 pbmc3k_scran_wilcox_any <- readRDS(
-  here::here("results", "real_data", "pbmc3k-scran_wilcox_any.rds")
+  here::here("results", "real_data", "pbmc3k-scran_findMarkers_wilcox_any.rds")
 )
 
 pbmc3k_scran_binom_any %>% 
@@ -65,7 +65,7 @@ wrap_plots(nkg7k_exps_plot, tyrobp_exps_plot, guides = "collect")  +
 ```{r}
 pbmc3k_sim_1 <- readRDS(here::here("data", "sim_data", "standard_sim_1-pbmc3k.rds"))
 pbmc3k_sim_1_scran_binom_any <- readRDS(
-  here::here("results", "sim_data", "standard_sim_1-pbmc3k-scran_binom_any.rds")
+  here::here("results", "sim_data", "standard_sim_1-pbmc3k-scran_findMarkers_binom_any.rds")
 ) 
 
 pbmc3k_sim_1_scran_binom_any %>% 

analysis/ss3-pbmc-expert-analysis.Rmd

@@ -158,7 +158,7 @@ plotExpression(ss3_pbmc, x = "label", features =  c("PRDM1", "IRF4")) +
 
 ```{r}
 scran_wilcox_any <- readRDS(
-  here::here("results", "real_data", "ss3_pbmc-scran_t_all.rds")
+  here::here("results", "real_data", "ss3_pbmc-scran_findMarkers_t_all.rds")
 )
 scran_wilcox_any$result %>% 
   filter(cluster == "Cytotoxic T")

analysis/zeisel-expert-analysis.Rmd

@@ -144,7 +144,7 @@ interneuron_seurat_t
 
 ```{r not-found-scran-t-any-interneurons-markers}
 scran_t_any <- readRDS(
-  here::here("results", "real_data", "zeisel-scran_t_any.rds")
+  here::here("results", "real_data", "zeisel-scran_findMarkers_t_any.rds")
 )
 
 scran_t_any$result %>%