scVelo 也是分析RNA速度的软件
四，Monocle2 Seurat
http://cole-trapnell-lab.github.io/monocle-release/
这两个都是分析单细胞的包

五 Scran AUCell
Bioconductor的包

六 Harmony
https://github.com/immunogenomics/harmony
Harmony is an algorithm for performing integration of single cell genomics datasets
对单细胞进行集成

七 NicheNetR
https://github.com/saeyslab/nichenetr
nichenetr: the R implementation of the NicheNet method. The goal of NicheNet is to study intercellular communication from a computational perspective.

八 pySCENIC
pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

九 scFEA
scFEA: A graph neural network model to estimate cell-wise metabolic using single cell RNA-seq data
十 NATMI
https://github.com/asrhou/NATMI
NATMI: Network Analysis Toolkit for the Multicellular Interactions
七到十都是一些下游分析的包

十一 数据格式
Seuratdisk
Interfaces for HDF5-based Single Cell File Formats
loomR