Table 2 Included R and python packages for different modules in SRT-Server
From: SRT-Server: powering the analysis of spatial transcriptomic data
Modules/Utilities | Packages |
|---|---|
Input/Output (IO) | hdf5r |
Quality Control (QC) | Seurat, dplyr, bigreadr |
Deconvolution (DECON) | CARD, hdf5r, plyr, gtools bigreadr, dplyr, SingleCellExperiment |
Deconvolution (DECON_py) | os, numpy, pandas, anndata, h5py, scipy, re, cell2location, tangram |
DECON_Plot | hdf5r, dplyr, bigreadr, ggplot2, scatterpie, SingleCellExperiment |
Spatially Variable Genes (SVG) | SPARK, dplyr, amap, spdep |
SVG_Plot | Seurat, ggplot2, dplyr, viridis, tidyr, reshape2, scales |
Cell Typing (CT) | Seurat, SeuratDisk, BASS, scSorter, monocle, garnett, org.Hs.eg.db, org.Mm.eg.db, glmGamPoi, dplyr, hdf5r, plyr |
Spatial Domain Detection (SDD) | BASS, SpatialPCA, dplyr |
CT_Plot and SDD_Plot | Seurat, hdf5r, dplyr, bigreadr, ggplot2 |
Differentially Expressed Genes (DE) | Seurat, hdf5r, dplyr, bigreadr |
DE_Plot | hdf5r, dplyr, bigreadr ComplexHeatmap, viridis, circlize, reshape2 |
Cell Cell Communication (CCC) | hdf5r, SpaTalk, liana, bigreadr, dplyr, SingleCellExperiment, Giotto |
CCC_Plot | CellChat, bigreadr, dplyr |
Over Representative Analysis (ORA) | clusterProfiler, ReactomePA, DOSE, org.Mm.eg.db, org.Hs.eg.db, dplyr, tibble, Matrix, bigreadr |
Psudo-time Trajectory (TRAJ) | Slingshot, SingleCellExperiment, tradeSeq, BiocParallel, Seurat, hdf5r, stringr, dplyr, tibble, tidyr, bigreadr |
TRAJ_Plot | hdf5r, ggplot2, bigreadr, dplyr, ComplexHeatmap, viridis, circlize, tidyr, reshape2, scales, ggtree, aplot, patchwork |