styler scRNAqc

Author: lpantano

01_quality_assessment/scRNA_QC.qmd

@@ -98,8 +98,6 @@ if (isUrl(params_file)) {
 }
 ```
 
-
-
 ```{r load}
 if (isUrl(seurat_obj)) {
   seurat_raw <- readRDS(url(seurat_obj))
@@ -108,7 +106,6 @@ if (isUrl(seurat_obj)) {
 }
 ```
 
-
 ```{r find doublets}
 #| eval: false
 # if you suspect that your dataset contains doublets, you can use this code to
@@ -148,7 +145,6 @@ seurat_qc <- subset(
 )
 ```
 
-
 ```{r filter ribo}
 #| eval: !expr ribosomal
 #| warning: false
@@ -164,13 +160,11 @@ seurat_qc <- subset(
 )
 ```
 
-
 ```{r}
 ## Save QC object
 saveRDS(seurat_qc, file = params$seurat_obj_filt_fn)
 ```
 
-
 ```{r prep-info}
 metadata0 <- [email protected]
 metadata0 <- metadata0 %>% dplyr::rename(
@@ -184,12 +178,10 @@ metadata1 <- metadata1 %>% dplyr::rename(
 )
 ```
 
-
 # QC metrics: raw data {.tabset}
 
 In this section, we review quality control (QC) metrics for the **raw feature matrices** generated by `Cellranger`. Only a low level filter excluding cells with <100 nUMIs (= number of unique molecular identifiers, or sequenced reads per cell) was applied when uploading the data into `R`. 
 
-
 ## Cells per sample
 
 ```{r cells raw}