Notebook resources

List of notebook resources

A list of all the notebooks used by IGF for generating QC plots and analysis results can be found here.

Analysis name	Documentation	Example notebooks
Singlecell data analysis using Scanpy	Github docs	Scanpy - Clustering of 3K PBMC cells
Singlecell data analysis using Seurat (dev)	Help docs	Seurat - Clustering of 3k PBMC cells
RNA-Seq data analysis (dev)	Help docs	RNA-Seq data using STAR and DESeq2 RNA-Seq data using STAR and DESeq2 (using Dask)
Single cell TCR/RNA-seq data analysis using Scirpy (dev)	Github docs	Analysis of 3k T cells from cancer
GWAS data analysis using Hail (dev)	Help docs	Hail - GWAS Tutorial
Viral genome analysis (dev)	Help docs	Viral genome - building consensus genome Viral genome - MSA and phylogenetic tree Coronavirus - Phylogenetic tree of 153 genomes Viral genome analysis using Nextstrain

Note:

A laptop / desktop with any modern web browser is required to explore these notebooks
Binder provides a temporary environment for running these example notebooks and any changes to the notebook will get deleted after a while
Start up time may vary for these notebooks as Binder needs to build a new environment once there are any new changes in these repositories
Repositories with tag dev are still under active development and the notebook runs may fail occasionally
All these notebooks will have Python/R/bash scripts. Although you can run these notebooks without knowing any of these programming languages, its recommended to have some basic knowledge, if you are planning to edit the code

You can run these notebooks on

Binder: Load these example notebooks using limited, free computational resource (using example data)
Docker (on your Laptop/Desktop): You will have to install Docker (https://docs.docker.com/get-docker/) on your own laptop or server, if you prefer to check your own data
Imperial College HPC: You have to install all the tools on a conda environment and then you can copy and run these notebooks on the HPC. More details on how to set up conda environment can be found here: https://www.imperial.ac.uk/admin-services/ict/self-service/research-support/rcs/support/applications/jupyter/

Note: Installing Docker will require root (admin) access on your laptop or server and you may need to contact the IT admin to complete this step.

Warning: Docker images downloaded from unknown sources can have malicious codes which can damage your laptop or server.