README.md

In jgockley62/UW_RNASeq: Identify differentially expressed genes counts data

RNA-seq normalization workflow in R

The sageseqr package integrates the drake R package, the config package for R, and Synapse. drake tracks dependency relationships in the workflow and only updates data when it has changed. A config file allows inputs and parameters to be explicitly defined in one location. Synapse is a data repository that allows sensitive data to be stored and shared responsibly.

The workflow takes RNA-seq gene counts and sample metadata as inputs, normalizes counts by CQN, removes outliers based on a user-defined threshold, empirically selects meaningful covariates and returns differential expression analysis results.

Access to Data

Anyone can create a Synapse account and access public data in a variety of disciplines: Alzheimer's Disease Knowledge portal, CommonMind Consoritum.

jgockley62/UW_RNASeq documentation built on Oct. 1, 2020, 8:07 p.m.