YUN's repositories
scanpy-python
Single-cell analysis in Python. Scales to >1M cells.
single-cell-best-practices-
This project is work in progress! https://www.sc-best-practices.org基于python的单细胞代码
single-cell-tutorial
基于python的单细胞代码流程
-cellrank
CellRank for directed single-cell fate mapping
-pyrovelocity
Probabilistic model of RNA velocity
-stLearn
A novel machine learning pipeline to analyse spatial transcriptomics data
awesome-R-R-
A curated list of awesome R packages, frameworks and software.
ccRCC_sn_publication
his github repository contains the data files and analysis code used in "Epigenetic and transcriptomic characterization reveals progression markers and essential pathways in clear cell renal cell carcinoma"
cNMF
Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
decoupleR-
R package to infer biological activities from omics data using a collection of methods.
get_internet_shengxin_paper
抓取网络文章到github issues保存 很多公众号文章都在这里
Giotto
Spatial omics analysis toolbox
HNSCC-
Analysis code used in Galeano Nino et al., Impact of Intratumoral Microbiota on Spatial and Cellular Heterogeneity in human cancer. 2022
METArisk-HNSCC-
Codes for METArisk
progeny-bulk
R package for Pathway RespOnsive GENe activity inference
RCC-spatial-mapping
Mapping single-cell transcriptomes in the intratumoral and associated territories of kidney cancer文章代码 空间转录组与侵袭前沿；NMF;Nichnet;和cell2loaction
RenalTumor
Single-cell multi-omics analysis reveals regulatory programs in clear cell renal cell carcinomaCD文章代码极好
scvelo-
RNA Velocity generalized through dynamical modeling
Seurat.utils-Seurat-
Various utility functions for Seurat single-cell analysis
SpatialDE-
Test genes for Spatial Variation 为python和scanpy设计
SpatialInferCNV
Clone Calling from Visium Spatial Transcriptomics of Cancer samples
stImage-
R package for integration analysis of spatial transcriptomics and morphology images可以借鉴代码
TCM-T-pancaner
Codes used in pan-T cell analysis
transcriptutorial-
This is a tutorial to guide the analysis of RNAseq dataset using footprint based tools such as DOROTHEA, PROGENY and CARNIVAL
yunbokai.github.io
Here is Lab website of Cheng Wang.