Skip to content

Latest commit

 

History

History
72 lines (47 loc) · 3.06 KB

Walkthrough_Day3.md

File metadata and controls

72 lines (47 loc) · 3.06 KB
Raw

Table of Contents

  1. Activate environment for Brainomics day 3

  2. Explore the course material and start the notebook

  3. Solutions to the exercises



1. Activate environment for Brainomics day 3

  • You should already have cloned the Brainomics repository in the previous days. If you haven't done it yet, you can do it by running the following command:
git clone https://github.com/BrainOmicsCourse/2024.git

For day 3 we have a new container for the specific tasks of spatial transcriptomics. We will use the folder day3 as the home of the container. The path to the container will be shared with you in the chat and on the whiteboard. Open the terminal and execute the following commands, after modifying the path to the shared folder:

module load singularity/3.8.5
singularity exec -B /group/brainomics/ -H $HOME/BrainOmics2024/3_Day3  /group/brainomics/Container/courses_brainomics2_day3-0.0.1.sif /bin/bash

This should open a new terminal inside the container. You need to initialize the conda environment by running the following commands:

conda init
source ~/.bashrc
conda-env list # you should see a list of environments, including day3_env
conda activate day3_env

Now we activated our environment so we can start Jupyter Lab:

jupyter lab

Copy the URL from the terminal (including the token) and paste it in your browser. You should now see the Jupyter Lab interface.



2. Explore the course material and start the notebook

On day 3 of Brainomics we will explore methods for spatial transcriptomics data analysis. Within the folder of day 3 you will find:

  • spatial_day3.ipynb, the Jupyter notebook on which we will work today.
  • two scripts .py, with additional code for the preprocessing of some of the data used in the notebook.
  • folders containing the scripts of two of the packages will be using today: SpaGE and Bansky. You can find updates of the packages in the respective repositories: SpaGE and Bansky.
  • folders containing utility functions
  • a folder containing the notebook with the solutions to the exercise, both as .ipynb and compiled in html format.

You can open the notebook as we will be working mainly on it today. The notebook is divided in 4 sections:

  • Data loading and explorative data analysis
  • Prediction of spatial patterns for unmeasured genes using scRNA-seq data with SpaGE
  • Imputation of unmeasured genes with Tangram
  • Spatial clustering with Bansky

3. Solutions to the exercises

Solutions to the exercise are in the shared folder, you can copy them in day 3 folder by copying this command in the terminal:

rsync -cvr -p /group/brainomics/InputData/day3/Compiled $HOME/BrainOmics2024/3_Day3

You should now see the Compiled folder in the 3_Day3 folder. There's a compiled .ipynb and .html file with the solutions to the exercises.