Home

Welcome to the 2024 Cold Spring Harbor Single Cell Course wiki! (Navin lab parts).

We'll be covering most of the single-cell RNA seq and spatial transcriptomics parts of the course. Here are the list of workshops:

Workshop	Instructors
1.1 scRNA: Processing Basics	Yiyun Lin, Anna Casasent, and Chenling Tang
1.2 scRNA: Copy Number Inference	Yiyun Lin
1.3 scRNA: Integration	Ryan Mulqueen and Yiyun Lin
2.1 Spatial RNA: Visium	Ping Xu and Aatish Thennavan
2.2 Spatial RNA: Curio Seeker	Ping Xu and Aatish Thennavan
3.1 scDNA: CopyKit	Kris Wang

Lecture	Instructors
Introduction to Spatial Transcriptomics	Ping Xu
scDNA data analysis using CopyKit	Kris Wang

All workshops can also be run on the CSHL cluster through Singularity images/containers, which can be pulled to other environments with Singularity. However, this is not supported on older versions of macOS.

Therefore, the older iMac workstations have had RStudio and R 4.4* or 4.2* installed, as well as the libraries required for each of the hands-on workshops. If you would like to install R, RStudio, or Singularity on your own computer, TAs may be able to assist during off-hours for the course.

Note: different versions of R and different library dependencies are required for each workshop; therefore, we suggest you first try using the Singularity containers. If you only want to install one version, install R 4.4 and Seurat 5, as that will work best for the data analysis part of the workshops.

Installing instructions for singularity can be found here: https://docs.sylabs.io/guides/3.0/user-guide/installation.html.

Macs and Windows machines require different virtual machines (VMs) in order to have the correct Linux kernel to run Singularity. After the VM is operational, you can install each of the environments.

To download the environments just run the following code:

singularity pull library://rmulqueen/cshl_course/scrna:latest #for scrna workshops
singularity pull library://rmulqueen/cshl_course/scdna:latest #for scdna workshops
singularity pull library://kris69w/cshl_course/spatial_celltrek:latest #for visium spatial workshops
#singularity pull library://rmulqueen/cshl_course/spatial:latest #for curio spatial workshops #not yet hosted

Thanks from the Navin lab team and hopefully it goes smoothly!!

Our on-site instructors:

Nick	Aatish	Ryan	Ping	Yiyun	Kris

Our off-site instructors:

Anna	Mitchell	Chenling	Jerome	Siyuan