This repository serves as the starting point for creating a GitHub-integrated Capsule for preprocessing and exploratory analysis of single cell data from four human innate T cells.
Choose the Python and R (Jupyterlab/RStudio) (3.10.12, R 4.2.3, JupyterLab 3.6.2, RStudio 2022.07.0-548) starter environment and add the following packages to the appropriate package manager:
mamba
r-irkernel=1.3.2
r-presto=1.0.0
r-rcpp=1.0.11
r-seurat=5.1.0
R (CRAN)
markdown=2.0
Bioconductor
BiocVersion=3.16.0
limma=3.54.2
Running this Rmd requires a data asset which can be created from the following S3 storage:
S3 bucket: codeocean-public-data
Path: example_datasets/innate_Tcell_transcriptome/
Data Asset Metadata
Title: Innate T Cell RNA-Seq Counts
Folder name: counts
Description: Low input RNA-seq and single-cell RNA-seq data from four human innate T cell. Initially retrieved from NCBI: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE124731
Note: do not import this repository directly. Instead, create a new repo from this template.
Notebook based on the original Scanpy Tutorial.