Chapter 2 Installation

SpaceSequest can be installed through a conda environment. We have tested the installation on Linux servers. Please ensure Conda is available on your device:

which conda
# Your conda path will be returned

Then navigate to the directory you would like to install the pipeline ($PipelineDir in the following example), and execute the following commands:

git clone https://github.com/interactivereport/SpaceSequest.git
cd SpaceSequest

# This step may take a while. Thank you for your patience
bash install.sh

# The .env will be created under the src directory
ls $PipelineDir/SpaceSequest/src/.env

#Add pipeline scripts to $PATH
vim ~/.bash_profile
PATH=$PATH:$PipelineDir/SpaceSequest
# Close the vim text editor and source the file
source ~/.bash_profile

#To verify the installation, type the name of one of the main scripts, such as:
visium

#Output:
=== Welcome to 'visium' from SpaceRequest! ===
    Please provide either a path to a folder or a config file.
    An empty config file will be created if a path to a folder is provided.

There are six workflows that can be directly used after successful installation of SpaceSequest:

  • visium: Process and analyze 10x Genomics Visium data using Space Ranger outputs.

  • visiumhd: Process and analyze 10x Genomics Visium HD data using Space Ranger outputs.

  • xenium: Analyze 10x Genomics Xenium data generated by Xenium Ranger.

  • cosmx: Analyze NanoString CosMx data using key files generated by the instrument.

  • geomx: Analyze NanoString GeoMx data using dcc files, which are converted from Fastq sequencing files.

  • cosMx2VIP: A converter script that incorporates CosMx data and high-resolution images to an h5ad output, which can be further explored by Cellxgene VIP.

Additionally, we also developed a new function, named getVisiumHDspotCol, to extract RGB color from the Visium HD bins, when a high-resolution image is provided. Detailed tutorials on how to used these workflows/scripts are provided in this Bookdown document.