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scATAC‐seq and scRNA‐seq data integration

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Ayushi Agrawal edited this page Oct 14, 2024 · 2 revisions

Description

This hands-on workshop will provide an introduction to integrating single-cell ATAC-seq data and single-cell RNA-seq data.

Required experience:

  1. Prior attendance to scRNA-seq, bulk RNA-seq workshops or experience with analysis of transcriptomics data
  2. Prior attendance at the Introduction to scATAC-seq data analysis workshop, or experience with analysis of scATAC-seq data
  3. Familiarity with R and RStudio (e.g., reading in files, working with lists and dataframes)

Learning Path

Advanced   This is an advanced workshop building upon the RNA-Seq Analysis series. Prior experience with scRNA-seq or bulk RNA-seq is required. See introductory and intermediate workshops in the RNA-Seq Analysis series.

Materials

Note: The download materials for this workshop are huge. Please make sure you have ~10-15 GB of free space on your computer before downloading these materials.

  1. There is a zip file with code and data at this link.
  2. Open the link, press the download button (usually on the top right corner), and select “Direct Download” if a menu pops up.
  3. The zip file download should start.
  4. Unzip the zip file.

Pre-workshop Instructions

  1. Install R and RStudio
  2. Install ArchR in RStudio using the instructions here.
  3. Install the required packages in RStudio:
BiocManager::install(version = "3.19", force=TRUE)
BiocManager::install("BSgenome.Hsapiens.UCSC.hg38")
install.packages('knitr', dependencies = TRUE)
install.packages("hdf5r")
install.packages('Seurat')
install.packages('tidyverse')
install.packages('patchwork')
install.packages('magrittr')
install.packages("Matrix", type = "source")
install.packages("irlba", type = "source")
require(devtools)
devtools::install_github("GreenleafLab/chromVARmotifs")
# install ggplot2 version 3.4.4 newer versions of ggplot2 are not compatible with ArchR package
install_version("ggplot2", version = "3.4.4", repos = "http://cran.us.r-project.org")
  1. Restart RStudio.
  2. Open the “1_preprocess_scRNAseqdata.Rmd” file (download here as explained above) in RStudio.
  3. Press the Knit button.
  4. Repeat steps 5-6 for "2_create_arrow_files_scATACseqdata.Rmd" and "3_ArchR_analysis_scATACseqdata.Rmd".

Note: If you see a warning about installing from source, respond with ‘y’ for yes

If your installations were successful, RStudio will run all the steps and compile an HTML document - one for each of the 3 Rmd files that were knit. It may take some time to run through all the steps.

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