Walkthroughs

Officially supported walkthroughs

The following walkthroughs were created by the sleuth team and demonstrate several use cases of sleuth. The code for generating each walkthrough is available on GitHub.

• Getting started with sleuth
  • Install and set up sleuth
  • How to perform a two condition differential analysis
  • Linking transcript IDs to genes
  • sleuth live
  • Basic QC
• Differential analysis using p-value aggregation, on multiple conditions and covariates
  • Testing frameworks for experimental designs with multiple conditions and covariates
  • Performing gene-level and transcript-level differential analyses that are consistent with each other by using p-value aggregation

Older walkthroughs

• These tutorials do not follow the new user interface for sleuth v.0.30.0 but we keep them here because we believe them to be instructive. We will likely update these tutorials at a later time to reflect the new user interface.
• Accounting for batch effects
  • Accounting for known batch effects
  • Extracting effect sizes (fold changes)
• Differential analysis with multiple conditions and covariates
  • Testing frameworks for experimental designs with multiple conditions and covariates
  • Performing gene-level differnetial analysis
  • Identifying and removing outliers

Community contributed walkthroughs

• Combining data from multiple RNA-Seq experiments
• Timecourse analysis