Course Overview


Course Integrity

This course is compiled automatically on 2024-07-15

The course is tested and available on MacOS, Windows and Ubuntu Linux for R version 4.4.0 (2024-04-24)



Overview

In this course we are going to introduce basic analysis for single-cell RNAseq, with a specific focus on the 10X system. The course is divided into three sessions. In the first session, we will introduce how to interpret the Cell Ranger QC report and how to do analysis with the LOUPE Browser. We will also demonstrate the customized analysis we can support right know. In the Second session, we will demonstrate how to process scRNAseq data and make QC reports with Seurat. In the third session, we will discuss how to to do more advanced analysis and QC with Bioconductor packages.

Exercises and answer sheets are included to help you practice techniques and provide examples.

Course material and exercises are available to view as rendered HTML at https://rockefelleruniversity.github.io/scRNA-seq/. All material is available to download under GPL v2 license.



Setting up


System Requirements

Install R

R can be installed from the R-project website.

The R website can be found here http://www.r-project.org/. This website has all the latest information about R updates, conferences and installation

You can use this direct links to the install for each major OS:


Install RStudio

RStudio can be installed from the RStudio website.

http://www.rstudio.com/

RStudio can be downloaded for all platforms at the link below

https://rstudio.com/products/rstudio/download/


Install required R packages

R Packages can be installed from the course package or from CRAN/Bioconductor. These commands should be written into the R console. Once R and RStudio is installed, you can copy and paste these install commands into lower left pane of RStudio which should be labelled “Console”. If you run into any errors, do this one line at a time.

From the course package
install.packages('BiocManager')
install.packages('remotes')
BiocManager::install('RockefellerUniversity/scRNA-seq',subdir='scRNASeq')
From CRAN and Bioconductor
install.packages('BiocManager')
BiocManager::install('DropletUtils')
BiocManager::install('scDblFinder')
BiocManager::install('SingleCellExperiment')
BiocManager::install('scran')
BiocManager::install('scater')
BiocManager::install('Seurat')
BiocManager::install('dplyr')
BiocManager::install('scuttle')
BiocManager::install('biomaRt')
BiocManager::install('hdf5r')
BiocManager::install('harmony')
BiocManager::install('scCustomize')
BiocManager::install('decontX')
BiocManager::install('bluster')
BiocManager::install('batchelor')
BiocManager::install('knitr')
BiocManager::install('rmarkdown')
BiocManager::install('testthat')
BiocManager::install('yaml')

Download the material

Download the material




The Presentations


Single-cell RNA sequencing , Session 1

In this session we will cover the use of Cell Ranger and the LOUPE browser.

Single-cell RNA sequencing , Session 2

In this session we will cover data processing with Seurat, including:

  • Basic QC, including mitochondrial content and cell cycle
  • Normalization and clustering
  • Visualization

Single-cell RNA sequencing , Session 3

In this session we will cover data processing with Bioconductor pacakges, including:

  • Empty droplet removal
  • Ambient RNA removal
  • Doublet removal

Single-cell RNA sequencing , Session 4

In this session we will cover scRNA processing in python from the R session using the R reticulate package and the python AnnData and Scanpy packages:

  • Introduction to reticulate package.
  • Loading scRNA data to AnnData objects.
  • Processing scRNA as AnnData in Scanpy.
  • Export of Scanpy processed AnnData to Loom.
  • Import of Loom to SingleCellExperiment.

Getting help


Course help

For advice, help and comments for the material covered in this course please contact us at the issues page associated to this course.

The link to the help pages can be found here


General Bioinformatics support

If you would like contact us about general bioinformatics advice, support or collaboration, please contact us the Bioinformatics Resource Center at .