Here we will collect pipelines for different analyses.

The below will primarily discuss working with data generated by the UofM Advanced Genomics Core. Customizations may be needed for data generated in other ways.

Table of contents

• Transcriptomics
  • Bulk
  • Single-cell
  • Spatial

Code will be a mixture of programming languages depending on the packages and environments used, with the primary language for analysis being R.

Transcriptomics

Bulk RNA

File Download

Aaron guide one and downloadable Rmd

Download works the Rmd file is changed when loading into R

Interactive R session link hosted on Google colab

Single-cell

Common packages:

• Seurat
• …

Pipelines/Scripts

• Basic Processing
  • from 10X
  • other data source
• Visualization
  • Scatter plots
  • Violin plots
  • Upset plots
• Integration
• Differential Expression
• Pseudotime & Velocity
• Cell-cell communication
• Comparison to external datasets
• GO/GSEA/etc

Others:

• Downloading data from publications
  • GEO
  • Other repositories

Spatial

At a later date

Proteomics

Epigenetics