Gitlab is now using https://gitlab.lcsb.uni.lu as it's primary address. Please update your bookmarks. FAQ.

Commit 96a9598c authored by Dimitrios Kyriakis's avatar Dimitrios Kyriakis
Browse files

No commit message

No commit message
parent ba7c3fc1
markdown: kramdown
kramdown:
parse_block_html: true
# PINK1 shows LRRK2, Parkin, and SNCA as part of the Parkinson’s network.
......@@ -40,8 +36,7 @@ EBs are cells at an early stage of spontaneous differentiation. Scorecard analys
## Libraries
<details><summary>Code</summary>
<p>
```r
```{r libraries}
library(reticulate)
use_python("C:/Users/dimitrios.kyriakis/AppData/Local/Continuum/anaconda3/envs/iscwrapper/python.exe", required = TRUE)
options(future.globals.maxSize= 2122317824)
......@@ -60,7 +55,6 @@ library(ggplot2)
library(ggpubr)
library(cowplot)
set.seed(123)
```
</p>
</details>
......@@ -69,8 +63,7 @@ set.seed(123)
## Setting Up
<details><summary>Code</summary>
<p>
```r
```{r setup}
# ================================ SETTING UP ======================================== #
tool="seurat"
project ="Michi_Data"
......@@ -99,7 +92,6 @@ SCT=TRUE
criteria_pass=3
min.cells <- 10
min.features <- 200
```
</p>
</details>
......@@ -113,7 +105,7 @@ Additional to this filtering, we defined cells as low-quality, based on three cr
<details><summary>Code</summary>
<p>
```r
```{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)
dir.create(NewDir)
......@@ -129,7 +121,6 @@ Return_fun <- ICSWrapper::create_cds2(list_of_files=list_of_files,
Combined <- Return_fun$Combined
Data_List <- Return_fun$Data_List
setwd("../")
```
</p>
</details>
......@@ -148,7 +139,6 @@ 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 =========================================
......@@ -173,7 +163,6 @@ Seurat.combined <- IntegrateData(anchorset = int.anchors, normalization.method =
DefaultAssay(object = Seurat.combined) <- "integrated"
Combined <- Seurat.combined
setwd("../")
```
</p>
</details>
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment