Commit 778f032c authored by Dimitrios Kyriakis's avatar Dimitrios Kyriakis
Browse files

collap

parent a1ff2df5
......@@ -37,6 +37,7 @@ EBs are cells at an early stage of spontaneous differentiation. Scorecard analys
<details><summary>Code</summary>
<p>
```r
library(reticulate)
use_python("C:/Users/dimitrios.kyriakis/AppData/Local/Continuum/anaconda3/envs/iscwrapper/python.exe", required = TRUE)
options(future.globals.maxSize= 2122317824)
......@@ -55,6 +56,7 @@ library(ggplot2)
library(ggpubr)
library(cowplot)
set.seed(123)
```
</p>
</details>
......@@ -64,6 +66,7 @@ set.seed(123)
<details><summary>Code</summary>
<p>
```r
# ================================ SETTING UP ======================================== #
tool="seurat"
project ="Michi_Data"
......@@ -92,6 +95,7 @@ SCT=TRUE
criteria_pass=3
min.cells <- 10
min.features <- 200
```
</p>
</details>
......@@ -106,6 +110,7 @@ Additional to this filtering, we defined cells as low-quality, based on three cr
<details><summary>Code</summary>
<p>
```r
# ======== Perform an integrated analysis ====
NewDir <- paste0(Sys.Date(),"_",tool,"_elbow_",elbow,"_Mito-",remove_mt,"_Ribo-",remove_ribsomal,"_SCT-",SCT,"_criteria_pass-",criteria_pass)
dir.create(NewDir)
......@@ -121,6 +126,7 @@ Return_fun <- ICSWrapper::create_cds2(list_of_files=list_of_files,
Combined <- Return_fun$Combined
Data_List <- Return_fun$Data_List
setwd("../")
```
</p>
</details>
......@@ -139,6 +145,7 @@ The integration of the filtered matrices of the different datasets was performed
<details><summary>Code</summary>
<p>
```{r remapping}
dir.create("Aligned_Cond_RegPhase")
setwd("Aligned_Cond_RegPhase")
# ================================== ALLIGN CONDITIONS =========================================
......@@ -163,6 +170,7 @@ Seurat.combined <- IntegrateData(anchorset = int.anchors, normalization.method =
DefaultAssay(object = Seurat.combined) <- "integrated"
Combined <- Seurat.combined
setwd("../")
```
</p>
</details>
......
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