Commit eda17661 authored by Dimitrios Kyriakis's avatar Dimitrios Kyriakis
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parent d52d770f
......@@ -35,7 +35,7 @@ EBs are cells at an early stage of spontaneous differentiation. Scorecard analys
## Libraries
<details>
<summary>Code</summary>
<summary>Code</summary>
```{r libraries, include=FALSE}
library(reticulate)
use_python("C:/Users/dimitrios.kyriakis/AppData/Local/Continuum/anaconda3/envs/iscwrapper/python.exe", required = TRUE)
......@@ -61,7 +61,7 @@ EBs are cells at an early stage of spontaneous differentiation. Scorecard analys
## Setting Up
<details>
<summary>Code</summary>
<summary>Code</summary>
```{r setup}
# ================================ SETTING UP ======================================== #
tool="seurat"
......@@ -102,7 +102,7 @@ Additional to this filtering, we defined cells as low-quality, based on three cr
<details>
<summary>Code</summary>
<summary>Code</summary>
```{r readfiles}
# ======== Perform an integrated analysis ====
NewDir <- paste0(Sys.Date(),"_",tool,"_elbow_",elbow,"_Mito-",remove_mt,"_Ribo-",remove_ribsomal,"_SCT-",SCT,"_criteria_pass-",criteria_pass)
......@@ -134,7 +134,7 @@ The integration of the filtered matrices of the different datasets was performed
<details>
<summary>Code</summary>
<summary>Code</summary>
```{r remapping}
dir.create("Aligned_Cond_RegPhase")
setwd("Aligned_Cond_RegPhase")
......@@ -171,7 +171,7 @@ The clustering of data was performed using Louvain clustering. The resolution of
<details>
<summary>Code</summary>
<summary>Code</summary>
```{r Clustering}
# ================================== Clustering =========================================
dir.create("Clusters")
......
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