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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
Single Cell Genomics Overview	Nick Navin
Introduction of R basics	Kris Wang
Introduction to Spatial Transcriptomics	Ping Xu
scDNA data analysis using CopyKit	Kris Wang

Running workshop locally

Workshop materials can be easily run on the iMacs in the Hershey lab and we highly recommend you to do so. We made a conda environment with all the r-packages pre-installed for the workshop. RStudio provides a user-friendly IDE for R-users. To launch RStudio, open a new terminal and make sure you are not in any conda environment by typing this in the terminal:

conda deactivate 

Then point RStudio to the R installed in the conda environment and launch RStudio IDE:

## run this if you are using iMac in Hershey Lab
export RSTUDIO_WHICH_R=/Users/admin/miniconda3/envs/course4.3/bin/R
## run this instead if you are using your own laptop 
export RSTUDIO_WHICH_R=/PATH/TO/WHERE/CONDA/INSTALLED/envs/course4.3/bin/R
open -na Rstudio

Running workshop on server

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 in the terminal:

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 --arch amd64 library://akcasasent/cshl_course/cellranger8.sif:latest
singularity pull library://kris69w/cshl_course/spatial:latest #for curio spatial workshops 

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