单细胞转录组及空间转录组学习资源

(1). 单细胞上游软件cellranger：单细胞上游软件cellranger从头说

(2). singleR操作说明：singleR

(3). seurat操作说明：seurat官网；seurat官方教程：seurat教程

(4). 多组学单细胞教程：OSCA

(5).单细胞课程：
scrnaseq-course
SingleCellWorkshop2020
NBIS-2021
youtube-videos
哈佛大学单细胞课程

(6).10x公司的案例video：video；案例

(7). 单细胞去除批次效应的软件合集文章：
A benchmark of batch-effect correction methods for single-cell RNA sequencing data，可白嫖GitHub上的操作：Github入口，上面有各类软件的测试数据和使用代码

(8).分析类流程：Current best practices in single‐cell RNA‐seq analysis: a tutorial

(9).单细胞细胞注释方法类文章：Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods

(10). 单细胞轨迹推断个人比较推荐使用dyno，因为该软件集合了很多种逆时间分析的算法，并且做成了shiny，网址：https://github.com/dynverse/dyno

(11). 单细胞下游分析软件合集：https://github.com/ZilongZhang44/single-cell-downstream-analysis

(12). A systematic evaluation of single cell RNA-seq analysis pipelines

(13). 单细胞差异基因比较pipeline，Confronting false discoveries in single-cell differential expression

(14). 李程教授学生写的单细胞pipeline：Single Cell Multi-Omics Data Analysis

(15). 基于UMI建库方式的上有pipeline：《Benchmarking UMI-based single-cell RNA-seq preprocessing workflows》

(16). 单细胞WGCNA：
github网站：https://github.com/smorabit/scWGCNA
在线教程：https://smorabit.github.io/tutorials/9_scWGCNA_tutorial

(17). Cell type and gene expression deconvolution with BayesPrism enables Bayesian integrative analysis across bulk and single-cell RNA sequencing in oncology | Nature Cancer https://www.nature.com/articles/s43018-022-00356-3

(18). metaVIPER||识别单细胞中的蛋白活性 - 生信编程日常 - 简书 https://www.jianshu.com/p/8eeb02758f2e

(19).Single-cell sequencing: expansion, integration and translation

(20). scGENA: A Single-Cell Gene Coexpression Network Analysis Framework for Clustering Cell Types and Revealing Biological Mechanisms》，这个流程相关的代码在 GitHub (https://github.com/zpliulab/scGENA)

(21). Python 单细胞分析流程：A molecular single-cell lung atlas of lethal COVID-19，
github：
1.https://github.com/IzarLab/CUIMC-NYP_COVID_autopsy_lung ；2.https://github.com/mousepixels/sanbomics_scripts；3.https://github.com/mousepixels/sanbomics_scripts/blob/main/single_cell_analysis_complete_class.ipynb

(22). 附加一个空间转录组的教程：空间转录组教程

(23). 单细胞RNA-seq与单细胞ATAC-seq联合分析例子：1. https://github.com/hcph/wheat_singlecellAtlas；2. https://github.com/rargelaguet/mouse_organogenesis_10x_multiome_publication

(24). 兔子scRNA和scATAC联合分析案例：《An atlas of rabbit development as a model for single-cell comparative genomics》，codes：https://github.com/MarioniLab/RabbitGastrulation2022

(25). High dimensional weighted gene co-expression network analysis ，hdWGCNA：https://github.com/smorabit/hdWGCNA