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Dimitrios Kyriakis
iPSCs_PINK1
Commits
a1ff2df5
Commit
a1ff2df5
authored
May 27, 2020
by
Dimitrios Kyriakis
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README.md
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a1ff2df5
...
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@@ -36,7 +36,7 @@ EBs are cells at an early stage of spontaneous differentiation. Scorecard analys
## Libraries
<details><summary>
Code
</summary>
<p>
```
{r libraries, include=FALSE}
```
r
library
(
reticulate
)
use_python
(
"C:/Users/dimitrios.kyriakis/AppData/Local/Continuum/anaconda3/envs/iscwrapper/python.exe"
,
required
=
TRUE
)
options
(
future.globals.maxSize
=
2122317824
)
...
...
@@ -63,7 +63,7 @@ set.seed(123)
## Setting Up
<details><summary>
Code
</summary>
<p>
```
{r setup}
```
r
# ================================ SETTING UP ======================================== #
tool
=
"seurat"
project
=
"Michi_Data"
...
...
@@ -105,7 +105,7 @@ Additional to this filtering, we defined cells as low-quality, based on three cr
<details><summary>
Code
</summary>
<p>
```
{
r
readfiles}
```
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
)
...
...
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