This repository is meant to serve as a template for single cell RNAseq projects. The goal is to align code across projects and analysts to speed up analyses and ensure consistent, quality science.
Before using this repository, please see the following entries in the knowledgebase for how to set up a successful project smoothly:
Dockerized Rstudio: Isolated containers with consistent architecture, R versions, and machine dependencies for essential libraries (e.g. DESeq2, Seurat).
Renv: Track versions of R libraries used for a project and enable a cache of different versions for different projects.
Format files: Workflow for rendering HTML reports.
Git and GitHub with RStudio (server): Getting git credentials setup in RStudio server, troubleshooting common git/GitHub/RStudio problems, and creating new gencore analysis projects from templates.
Template repos: Directory structure and scripts generalizable to an analysis. These serve as starting points for new analyses.
Gencore packages: Standardized code for common gencore analyses.