EMBL_workshop_2025

A workflowr project.

Welcome to the homepage for the 2025 Spatial Transcriptomics website.

Schedule

Morning

Visium HD

We'll run:

1. Space Ranger on Pawsey
2. Loupe Browser on your local laptops :)
3. R (through Singularity) on Pawsey

Afternoon

Xenium

• Xenium part 1
• Xenium part 2
• Xenium part 3

Tip, make RBioformats work by running this line:

dyn.load('/usr/lib/jvm/default-java/lib/server/libjvm.so')

Setup

You will be given a username and password to login on the day.

You then have two options for connecting:

1. ssh in directly, using [email protected]

2. connect to an RStudio instance already running via your browser: https://embl.sagc-dataviz.cloud.edu.au/username

SSH setup

To ssh in directly, you need an ssh client installed.

Windows

The latest builds of Windows 10 and 11 come with SSH server and client. To see if your windows installation has SSH:

• start Command Prompt (cmd) or Powershell
• type in 'ssh'

If SSH is available, you should see something like

usage: ssh [-46AaCfGgKkMNnqsTtVvXxYy] [-B bind_interface]
           [-b bind_address] [-c cipher_spec] [-D [bind_address:]port]
           [-E log_file] [-e escape_char] [-F configfile] [-I pkcs11]
           [-i identity_file] [-J [user@]host[:port]] [-L address]
           [-l login_name] [-m mac_spec] [-O ctl_cmd] [-o option] [-p port]
           [-Q query_option] [-R address] [-S ctl_path] [-W host:port]
           [-w local_tun[:remote_tun]] destination [command]

If SSH is not available, please install PuTTY.

Open PuTTY and connect using setonix.pawsey.org.au as the host name, and set port to 22.

When prompted, type in your username and password.

macOS

Use ssh in the Terminal app. For example, if your user name is user, you would enter:

ssh [email protected]

When prompted, type your password and then press return.

Linux

Same as macOS, an SSH client should be included. If not, install via the default package manager. e.g.:

# ubuntu
sudo apt install openssh-client

Xenium data

https://www.10xgenomics.com/platforms/visium/product-family/dataset-human-crc

wget https://cf.10xgenomics.com/samples/xenium/2.0.0/Xenium_V1_Human_Colon_Cancer_P5_CRC_Add_on_FFPE/Xenium_V1_Human_Colon_Cancer_P5_CRC_Add_on_FFPE_outs.zip