This repository serves as the starting point for creating a GitHub-integrated Capsule for preprocessing and exploratory analysis of single cell data from 2700 Peripheral Blood Mononuclear Cells.
Choose the Python and R (Jupyterlab/RStudio) (python3.10.12-R4.2.3-IRkernel-ubuntu22.04) starter environment and add the following packages to the mamba package manager:
anndata==0.9.2
leidenalg==0.10.1
matplotlib==3.7.2
pandas==2.0.3
scanpy==1.9.5
Running this notebook requires a data asset which can be created from the following S3 storage:
S3 bucket: codeocean-public-data
Path: example_datasets/single-cell-tutorial/pbmc3k/filtered_gene_bc_matrices/
Data Asset Metadata
Title: Single Cell Tutorial - 3k PBMCs
Folder name: filtered_gene_bc_matrices
Description: Peripheral Blood Mononuclear Cells (PBMC) dataset freely available from 10X Genomics. There are 2,700 single cells that were sequenced on the Illumina NextSeq 500. The raw data can be found at https://cf.10xgenomics.com/samples/cell/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz
Note: do not import this repository directly. Instead, create a new repo from this template.
Notebook based on the original Scanpy Tutorial.