List of software packages for single-cell RNA-seq analysis List of workflow and tutorials for single-cell RNA-seq analysis
- Monocle - [R] - Differential expression and time-series analysis for single-cell RNA-Seq.
- scater - [R] - Scater places an emphasis on tools for quality control, visualisation and pre-processing of data before further downstream analysis, filling a useful niche between raw RNA-sequencing count or transcripts-per-million data and more focused downstream modelling tools such as monocle, scLVM, SCDE, edgeR, limma and so on.
- Seurat - [R] - It contains easy-to-use implementations of commonly used analytical techniques, including the identification of highly variable genes, dimensionality reduction (PCA, ICA, t-SNE), standard unsupervised clustering algorithms (density clustering, hierarchical clustering, k-means), and the discovery of differentially expressed genes and markers.
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Aaron Lun's Single Cell workflow on Bioconductor - [R] - This article describes a computational workflow for basic analysis of scRNA-seq data using software packages from the open-source Bioconductor project.
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Cole Trapnell's Single Cell workflow - [R] - Monocle introduced the strategy of ordering single cells in pseudotime, placing them along a trajectory corresponding to a biological process such as cell differentiation by taking advantage of individual cell's asynchronous progression of those processes.
example:
Reproducing the original pseudo-time clustering plot in Shiny :https://nyhuyang.shinyapps.io/single_cell_clusters/
Distribution based on gene expression levels (y-axis) in Shiny: https://nyhuyang.shinyapps.io/single_cell_expression/ -
Hemberg lab's Analysis of single cell RNA-seq data - [R] - This course we will discuss some of the questions that can be addressed using scRNA-seq as well as the available computational and statistical methods avialable. The course is taught through the University of Cambridge Bioinformatics training unit
- 【陈巍学基因】视频56：X10 genomics分析单细胞表达 - [Youtube] - 介绍10X genomics系统，和用10X genomics来对一大群细胞（几 千个）当中每个单细胞的表达进行定量分析的工作原理。