Table 1 Summary of analysis tools used in Shaoxia
From: Shaoxia: a web-based interactive analysis platform for single cell RNA sequencing data
Stage | Step | Command | Software tool |
|---|---|---|---|
Upstream analysis | Reads mapping | cellranger count | 10X Genomics cellranger |
Generate loom | samtools sort velocyto run10x | Samtools [16] scvelo Python package [17] | |
Quality control | Seurat::PercentageFeatureSet | Seurat R package [11] | |
Integration | Seurat::FindIntegrationAnchors | Seurat R package [11] | |
Merge | Seurat::merge | Seurat R package [11] | |
Dimension reduction & clustering | Seurat::FindVariableFeatures Seurat::NormalizeData Seurat::ScaleData Seurat::RunPCA Seurat::FindNeighbours Seurat::FindClusters Seurat::RunUMAP | Seurat R package [11] | |
Cell annotation | Cell type annotation | - | Seurat R package [11] |
Cell subtype annotation | - | Seurat R package [11] | |
Downstream analysis | inferCNV | infercnv::run | infercnv R package [18] |
Cluster correlation | ComplexHeatmap:: Heatmap | ComplexHeatmap R package [19] | |
Cell cycle scoring | Seurat::CellCycleScoring | Seurat R package [11] | |
Cell type frequency | ggplot2::geom_bar | ggplot2 R package [20] | |
KEGG & GO erichment | Seurat::FindMarkers ClusterProfiler::enrichKEGG ClusterProfiler::enrichGO | Seurat R package [11] ClusterProfiler [21] | |
GSVA | gsva:: gsva | gsva R package [22] | |
GSEA | gsea-cli.sh GSEA | GESA software [23] | |
Trajectory anlysis | monocle::setOrderingFilter monocle:: reduceDimension monocle:: orderCells monocle3::cluster_cells monocle3::learn_graph monocle3::order_cells | Monocle and Monocle3 R package [24] | |
RNA velocity | velocity_embedding_stream | scvelo Python package [17] | |
Cell communiction | cellphonedb method cellphonedb plot | cellphonedb Python package [12] | |
Gene regulation | pyscenic grn pyscenic ctx pyscenic aucell | SCENIC Python package [13] |