单细胞云平台涉及的软件调研分析

anneng

一，Kallisto
一个和Star功能类似的转录本统计分析软件
https://www.g3journal.org/content/10/5/1775
Evaluation of STAR and Kallisto on Single Cell RNA-Seq Data Alignment
Star 的效果比较好但是资源需求量是kallisto的几倍
二，Bustools
和Kallisto搭配使用最终生成统计矩阵 kallisto会生成一个BUS格式的文件 bustools用来处理这个文件
https://github.com/BUStools/BUS-format
https://www.kallistobus.tools/
三，Velocyto.py scVelo
http://velocyto.org/
velocyto (velox κύτος, quick cell) 是一个用于分析单细胞 RNA seq 数据中表达动态的软件包。特别是，它可以通过区分标准单细胞 RNA 测序协议中未剪接和剪接的 mRNA 来估计单细胞的 RNA 速度

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