QC Report
Yerly et al. (2022)
Raw Data
All Samples
Genes per cell
Globin fraction
Top 20 gene fraction
MT fraction
Ribosomal fraction
Total counts
Per Sample
QC metrics
Mitochondrial counts
Highest expressed genes
QC metrics
Mitochondrial counts
Highest expressed genes
QC metrics
Mitochondrial counts
Highest expressed genes
QC metrics
Mitochondrial counts
Highest expressed genes
QC metrics
Mitochondrial counts
Highest expressed genes
Filtered Data
All Samples
Genes per cell
Globin fraction
Top 20 gene fraction
MT fraction
Ribosomal fraction
Total counts
Per Sample
QC metrics (filtered)
Mitochondrial counts (filtered)
Highest expressed genes (filtered)
QC metrics (filtered)
Mitochondrial counts (filtered)
Highest expressed genes (filtered)
QC metrics (filtered)
Mitochondrial counts (filtered)
Highest expressed genes (filtered)
QC metrics (filtered)
Mitochondrial counts (filtered)
Highest expressed genes (filtered)
QC metrics (filtered)
Mitochondrial counts (filtered)
Highest expressed genes (filtered)
Doublets
Per Sample
Doublet score distribution
Doublet score statistics
Doublet score distribution
Doublet score statistics
Doublet score distribution
Doublet score statistics
Doublet score distribution
Doublet score statistics
Doublet score distribution
Doublet score statistics
Distribution
Normalisation effect
Statistical QC
Mean–variance relationship
QQ plots
Coefficient of variation
Cell–cell correlation
Feature Selection
Highly variable genes
HVG batch consistency
PCA
PCA variance ratio
Gene loadings by PC
PCA QC metrics
UMAP
UMAP QC metrics
Clustering resolutions
Results
Integration QC
Integration quality
UMAP
Label transfer UMAP
scANVI UMAP QC
Cell origin UMAP
Clustering
Clustering resolutions
Annotation QC (res 0.5)
Annotation QC (res 1.0)
Annotation QC (res 1.5)
Annotation QC (res 2.0)
Model Training
ELBO
KL divergence
Reconstruction loss