Recipes, SOPs, notes on best practices. Format inspired by https://github.com/hbc/knowledgebase/.
This repo should be living documentation that is updated with alternative methods as we discover them, but should preserve old methods for posterity and include rationale for changing them. Whenever possible, we should include links to papers, repos, vignettes, etc. that support a practice, and we should attempt to summarize the methods and justifications of a particular step. If we explore a procedure that we decide not to implement, it is worth including it here too to avoid revisiting dead topics and save others from wasting time.
Reading materials and tutorials for new hires
Using our servers, data management, etc.
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.
Cancer exome: Detecting mutations driving cancer
Cancer fusions: Detecting RNA fusions in tumor samples.
TCR Analysis: Identifying clonal expansion of T/B cells across treatments/timepoints.
RNA-seq model design: Designing linear models for your study.
Orthologous gene symbols: Finding the corresponding gene symbol across species (e.g. mouse -> human, human -> macaca mulatta)
Immunology cell types: Nomenclature for immune cells and aliases. See the image for an overview.
Gencore gene expression database: A collection of differentially expressed genes and celltype markers from Gencore projects.
S3 Storage: Recover files from glacier