scRNA-seq Analysis Report
📊 Dataset Overview
Summary9,798
Total Cells
14,589
Total Genes
2,000
HVGs
0
Med. Genes/Cell
0
Med. UMIs/Cell
7
Clusters
This single-cell RNA-seq dataset contains 9,798 cells and
14,589 genes. After quality control, 2,000 highly variable genes
(13.7% of total) were used for downstream analysis.
Analysis Progress
7/7 Steps
🔍 Quality Control
Metrics
| Parameter | Value |
|---|---|
| Mitochondrial threshold | 0.2% |
| Minimum UMIs | 500 |
| Minimum genes | 250 |
🧬 Gene Expression
HVGs
Highly Variable Genes: 2000 genes selected
(13.7% of total) for downstream analysis.
📈 Dimensionality Reduction
PCA
| Parameter | Value |
|---|---|
| Number of components | 50 |
| Data layer | scaled |
| Use HVGs | True |
🔄 Batch Correction
Integration
Best Method: X_scVI
selected as the optimal integration method.
🎯 Cell Clustering
7 Clusters
Identified 7 distinct cell clusters using SCCAF algorithm.
⏰ Cell Cycle Analysis
Distribution
⚙️ Analysis Pipeline
Status| Step | Status | Parameters |
|---|---|---|
| 🔍 Quality Control | Completed | batch_key: batch; detected_genes: 250 (+10) |
| ⚙️ Preprocessing | Completed | mode: shiftlog|pearson; n_HVGs: 2000 (+2) |
| 📏 Data Scaling | Completed | Default |
| 📈 PCA | Completed | layer: scaled; n_pcs: 50 |
| 🔄 Cell Cycle | Completed | g2m_genes: ['Cbx5' 'Aurkb' 'Cks1b' 'Cks2' 'Jpt1' 'Hmgb2' 'Anp32e' 'Lbr' 'Tmpo' 'Top2a' 'Tacc3' 'Tubb4b' 'Ncapd2' 'Rangap1' 'Cdk1' 'Smc4' 'Kif20b' 'Cdca8' 'Ckap2' 'Ndc80' 'Dlgap5' 'Hjurp' 'Ckap5' 'Bub1' 'Ckap2l' 'Ect2' 'Kif11' 'Birc5' 'Cdca2' 'Nuf2' 'Cdca3' 'Nusap1' 'Ttk' 'Aurka' 'Mki67' 'Pimreg' 'Ccnb2' 'Tpx2' 'Hjurp' 'Anln' 'Kif2c' 'Cenpe' 'Gtse1' 'Kif23' 'Cdc20' 'Ube2c' 'Cenpf' 'Cenpa' 'Hmmr' 'Ctcf' 'Psrc1' 'Cdc25c' 'Nek2' 'Gas2l3' 'G2e3']; s_genes: ['Cdca7' 'Mcm4' 'Mcm7' 'Rfc2' 'Ung' 'Mcm6' 'Rrm1' 'Slbp' 'Pcna' 'Atad2' 'Tipin' 'Mcm5' 'Uhrf1' 'Polr1b' 'Dtl' 'Prim1' 'Fen1' 'Hells' 'Gmnn' 'Pold3' 'Nasp' 'Chaf1b' 'Gins2' 'Pola1' 'Msh2' 'Casp8ap2' 'Cdc6' 'Ubr7' 'Ccne2' 'Wdr76' 'Tyms' 'Cdc45' 'Clspn' 'Rrm2' 'Dscc1' 'Rad51' 'Usp1' 'Exo1' 'Blm' 'Rad51ap1' 'Cenpu' 'E2f8' 'Mrpl36'] |
| 🎵 Harmony | Completed | n_pcs: 50 |
| 🧬 scVI | Completed | gene_likelihood: nb; n_latent: 30 (+1) |
| 📊 Benchmarking | Not Completed | Default |
| 🎯 Clustering | Not Completed | Default |
Generated by OmicVerse with Primordecode Team • 2025-06-07 19:23