diff --git a/01_quality_assessment/scRNA_QC.qmd b/01_quality_assessment/scRNA_QC.qmd index 0e9b43a..81c2acc 100644 --- a/01_quality_assessment/scRNA_QC.qmd +++ b/01_quality_assessment/scRNA_QC.qmd @@ -178,10 +178,12 @@ metadata1 <- metadata1 %>% dplyr::rename( ) ``` -# QC metrics: raw data {.tabset} +# QC metrics: raw data 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`. +:::{.panel-tabset} + ## Cells per sample ```{r cells raw} @@ -351,13 +353,16 @@ metadata0 %>% theme(plot.title = element_text(hjust = 0.5, face = "bold")) ``` +::: -# QC metrics: Filtered data {.tabset} +# QC metrics: Filtered data Based on the above QC metrics, we filtered the dataset to isolate cells passing the following thresholds: >`r nCount_RNA_cutoff` UMIs, >`r nFeature_RNA_cutoff` genes, <`r mitoRatio_cutoff` mitochondrial gene ratio, and >`r Log10GenesPerUMI_cutoff` complexity. In this section, we review QC metrics for our filtered dataset. +:::{.panel-tabset} + ## Cells per sample ```{r cells filtered} @@ -521,6 +526,7 @@ metadata1 %>% theme(plot.title = element_text(hjust = 0.5, face = "bold")) ``` +::: # R session