QC Report – Straalen et al. (2024)

QC Report

Straalen et al. (2024)

Raw Data

All Samples

Genes per cell

Genes per cell

$Globin fraction$

Globin fraction

$Top 20 gene fraction$

Top 20 gene fraction

$MT fraction$

MT fraction

$Ribosomal fraction$

Ribosomal fraction

Total counts

Total counts

Per Sample

QC metrics

Mitochondrial counts

Mitochondrial counts

Highest expressed genes

Highest expressed genes

QC metrics

Mitochondrial counts

Mitochondrial counts

Highest expressed genes

Highest expressed genes

QC metrics

Mitochondrial counts

Mitochondrial counts

Highest expressed genes

Highest expressed genes

QC metrics

Mitochondrial counts

Mitochondrial counts

Highest expressed genes

Highest expressed genes

QC metrics

Mitochondrial counts

Mitochondrial counts

Highest expressed genes

Highest expressed genes

QC metrics

Mitochondrial counts

Mitochondrial counts

Highest expressed genes

Highest expressed genes

QC metrics

Mitochondrial counts

Mitochondrial counts

Highest expressed genes

Highest expressed genes

QC metrics

Mitochondrial counts

Mitochondrial counts

Highest expressed genes

Highest expressed genes

QC metrics

Mitochondrial counts

Mitochondrial counts

Highest expressed genes

Highest expressed genes

Filtered Data

All Samples

Genes per cell

Genes per cell

$Globin fraction$

Globin fraction

$Top 20 gene fraction$

Top 20 gene fraction

$MT fraction$

MT fraction

$Ribosomal fraction$

Ribosomal fraction

Total counts

Total counts

Per Sample

QC metrics (filtered)

QC metrics (filtered)

Mitochondrial counts (filtered)

Mitochondrial counts (filtered)

Highest expressed genes (filtered)

Highest expressed genes (filtered)

QC metrics (filtered)

QC metrics (filtered)

Mitochondrial counts (filtered)

Mitochondrial counts (filtered)

Highest expressed genes (filtered)

Highest expressed genes (filtered)

QC metrics (filtered)

QC metrics (filtered)

Mitochondrial counts (filtered)

Mitochondrial counts (filtered)

Highest expressed genes (filtered)

Highest expressed genes (filtered)

QC metrics (filtered)

QC metrics (filtered)

Mitochondrial counts (filtered)

Mitochondrial counts (filtered)

Highest expressed genes (filtered)

Highest expressed genes (filtered)

QC metrics (filtered)

QC metrics (filtered)

Mitochondrial counts (filtered)

Mitochondrial counts (filtered)

Highest expressed genes (filtered)

Highest expressed genes (filtered)

QC metrics (filtered)

QC metrics (filtered)

Mitochondrial counts (filtered)

Mitochondrial counts (filtered)

Highest expressed genes (filtered)

Highest expressed genes (filtered)

QC metrics (filtered)

QC metrics (filtered)

Mitochondrial counts (filtered)

Mitochondrial counts (filtered)

Highest expressed genes (filtered)

Highest expressed genes (filtered)

QC metrics (filtered)

QC metrics (filtered)

Mitochondrial counts (filtered)

Mitochondrial counts (filtered)

Highest expressed genes (filtered)

Highest expressed genes (filtered)

QC metrics (filtered)

QC metrics (filtered)

Mitochondrial counts (filtered)

Mitochondrial counts (filtered)

Highest expressed genes (filtered)

Highest expressed genes (filtered)

Doublets

Per Sample

Doublet score distribution

Doublet score distribution

Doublet score statistics

Doublet score statistics

Doublet score distribution

Doublet score distribution

Doublet score statistics

Doublet score statistics

Doublet score distribution

Doublet score distribution

Doublet score statistics

Doublet score statistics

Doublet score distribution

Doublet score distribution

Doublet score statistics

Doublet score statistics

Doublet score distribution

Doublet score distribution

Doublet score statistics

Doublet score statistics

Doublet score distribution

Doublet score distribution

Doublet score statistics

Doublet score statistics

Doublet score distribution

Doublet score distribution

Doublet score statistics

Doublet score statistics

Doublet score distribution

Doublet score distribution

Doublet score statistics

Doublet score statistics

Doublet score distribution

Doublet score distribution

Doublet score statistics

Doublet score statistics

Distribution

Normalisation effect

Normalisation effect

Statistical QC

Mean–variance relationship

Mean–variance relationship

QQ plots

QQ plots

Coefficient of variation

Coefficient of variation

Cell–cell correlation

Cell–cell correlation

Feature Selection

Highly variable genes

Highly variable genes

HVG batch consistency

HVG batch consistency

PCA

PCA variance ratio

PCA variance ratio

Gene loadings by PC

Gene loadings by PC

PCA QC metrics

PCA QC metrics

UMAP

UMAP QC metrics

UMAP QC metrics

Clustering resolutions

Clustering resolutions

Results

Integration QC

Integration quality

Integration quality

UMAP

Label transfer UMAP

Label transfer UMAP

scANVI UMAP QC

scANVI UMAP QC

Cell origin UMAP

Cell origin UMAP

Clustering

Clustering resolutions

Clustering resolutions

Annotation QC (res 0.5)

Annotation QC (res 0.5)

Annotation QC (res 1.0)

Annotation QC (res 1.0)

Annotation QC (res 1.5)

Annotation QC (res 1.5)

Annotation QC (res 2.0)

Annotation QC (res 2.0)

Model Training

ELBO

ELBO

KL divergence

KL divergence

Reconstruction loss

Reconstruction loss