Others

Other resources

CSOmap: Ren, X., Zhong, G., Zhang, Q., Zhang, L., Sun, Y., and Zhang, Z. (2020). Reconstruction of cell spatial organization from single-cell RNA sequencing data based on ligand-receptor mediated self-assembly. Cell Research.
scrna-seq tools: scRNA-seq tool sets
Novogene scRNA-seq
Seurat: QC, analysis, and exploration of single cell RNA-seq data
Monocle: Differential expression and time-series analysis for single-cell RNA-Seq
ClusterMap
cell ranger: Single cell qc and mapping
Pagoda2
SCDE: Pathway and gene sets analysis using pangoda (Workshop)
cellphonedb: Receptors, ligands and its interactions
velocyto
SC3: A purely clustering tool
pcaReduce
scRNA-seq method note
UMI tools
umi
fgbio GroupReadsByUmi
UMI-Reducer
bseqsc: Deconvolution of Bulk Sequencing
XENA
Cten: Identify cell types
SingleR
SCANPY
DensityPath: Reconstruct the underlying cell developmental trajectories
scanpy
ASAP: Web-based scRNA-seq tool
scDNA: Single-cell mutation analysis of clonal evolution
monovar