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Dimitrios Kyriakis
iPSCs_PINK1
Commits
778f032c
Commit
778f032c
authored
May 27, 2020
by
Dimitrios Kyriakis
Browse files
collap
parent
a1ff2df5
Changes
1
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README.md
View file @
778f032c
...
...
@@ -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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