This repository contains istructions and material for the scRNAseq Hackathon, School of Mathematics, University of Leeds, 12/05/2022

• https://conferences.leeds.ac.uk/bad-hackathon/programme/

Pipelines

During the day we will follow 2 pipelines:

• Seurat Pipeline (md format)
• Monocle 3 Pipeline (md format)

Data Availability

Please download the following folder:

• Datasets Drive Folder

Sofware prerequisites

Required packages and software installation list:

R software:

• Latest R version (4.1.3 onwards) https://www.r-project.org/
• Rstudio (optional) https://www.rstudio.com/

R packages:

Open R\Rstudio and run the code highlighted

• Devools, Remotes R build tools

install.packages("devtools")
install.packages("remotes")
install.packages("pkgbuild")
install.packages("mclust")
pkgbuild::check_build_tools()

• Seurat

install.packages("Seurat")
devtools::install_github('satijalab/seurat-data')
remotes::install_github('satijalab/seurat-wrappers')

• DropletUtils

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("DropletUtils")

• DoubletFinder

remotes::install_github("chris-mcginnis-ucsf/DoubletFinder")

• Monocle3 installation on Windows OS

if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# Remove this 
# BiocManager::install(version = "3.10")

# Next, install a few Bioconductor dependencies that aren't automatically installed:

BiocManager::install(c('BiocGenerics', 'DelayedArray', 'DelayedMatrixStats',
                       'limma', 'S4Vectors', 'SingleCellExperiment',
                       'SummarizedExperiment', 'batchelor', 'Matrix.utils'))
# Now, install monocle3 through the cole-trapnell-lab GitHub, execute:

devtools::install_github('cole-trapnell-lab/leidenbase')
devtools::install_github('cole-trapnell-lab/monocle3')
# If you wish to install the develop branch of monocle3, execute:

devtools::install_github('cole-trapnell-lab/monocle3', ref="develop")

• Monocle3 installation on macOS Monterey Chip M1

R version 4.2.0 (2022-04-22)

Platform: aarch64-apple-darwin20 (64-bit)

Running under: macOS Monterey 12.3.1

1 - Install Xcode from the Appstore (it requires some time, almost one hour with good connection) 2 - After Xcode is installed, accept the license and the installation of additional components 3 - Open the terminal and run the command 'xcode-select --install' (almost 15/20 minutes)

Ignore "xcode-select: error: command line tools are already installed, use "Software Update" to install updates". It means that it is already installed.

4 - Download gfortran from https://github.com/fxcoudert/gfortran-for-macOS/releases/tag/11-arm-alpha2 (M1 processor) or from https://github.com/fxcoudert/gfortran-for-macOS/releases (Intel processor). The user-friendly installation package is gfortran-ARM-11.0-BigSur.pkg 5 - Click on the .pkg file to install gfortan in /usr/local/bin 6 - In the home directory, create a hidden directory called .R and create inside a file called 'Makevars'. In this file, write:

F77 = /usr/local/bin/gfortran
FC = $(F77)
FLIBS = -L/usr/local/gfortran/lib/gcc/aarch64-apple-darwin20.2.0

Check for the correspondence with your path, it might change from user to user.

7 - Proceed with Monocle3 installation and select 'no' at the following question:

Do you want to install from sources the packages which need compilation? (Yes/no/cancel)

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Monocole 3 Original Pipelines

http://cole-trapnell-lab.github.io/monocle-release/monocle3/#tutorial-1-learning-trajectories-with-monocle-3

http://cole-trapnell-lab.github.io/monocle-release/monocle3/#step-3-partition-the-cells-into-supergroups

Seurat Original Pipelines

https://satijalab.org/seurat/index.html

http://htmlpreview.github.io/?https://github.com/satijalab/seurat-wrappers/blob/master/docs/monocle3.html