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) (python3.10.12-R4.2.3-IRkernel-ubuntu22.04) starter environment and add the following packages to the mamba package manager with the bioconda channel:
bioconductor-biocversion=3.20.0
bioconductor-limma=3.62.1
r-biocmanager=1.30.25
r-irkernel=1.3.2
r-markdown=1.13
r-rcpp=1.0.14
r-seurat=5.1.0
To the R(GitHub) package manager, add:
immunogenomics/presto
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.