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  • Hall Lab Homepage
  • CLARITE Github Repo
  • Motivation
  • Installation
  • Citing CLARITE
  • Usage
  • Example Analysis
  • Complex Survey Data
  • Regression
  • API Reference
  • CLI Reference
  • Release History
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CLARITE Documentation¶

Version:1.1.1.post47+g0530ed3

CLeaning to Analysis: Reproducibility-based Interface for Traits and Exposures

  • Hall Lab Homepage
  • CLARITE Github Repo
  • Motivation
  • Installation
    • Basic Install
    • Running R code from CLARITE
  • Citing CLARITE
  • Usage
    • Organization of Functions
    • Coding Style
  • Example Analysis
    • Load Data
    • Define the phenotype and covariates
    • Initial cleanup / variable selection
    • QC
    • Checking the phenotype distribution
    • EWAS
    • Replication
    • Manhattan Plots
  • Complex Survey Data
    • Single Clusters
    • Missing Weights
    • Subsets
  • Regression
    • Regression Classes

API Reference¶

If you are looking for information on a specific function, class or method, this part of the documentation is for you.

  • API Reference
    • Analyze
    • Describe
    • Load
    • Modify
    • Plot
    • Survey

CLI Reference¶

Documentation for using the CLI

  • CLI Reference
    • –skip and –only
    • Commands

Additional Notes¶

Release History, etc

  • Release History
    • v1.1.1 (2020-06-12)
    • v1.1.0 (2020-08-14)
    • v1.0.1 (2020-06-12)
    • v1.0.0 (2020-06-04)
    • v0.10.0 (2020-05-28)
    • v0.9.1 (2019-11-20)
    • v0.9.0 (2019-10-31)
    • v0.8.0 (2019-09-03)
    • v0.7.0 (2019-07-23)
    • v0.6.0 (2019-07-11)
    • v0.5.0 (2019-06-28)
    • v0.4.0 (2019-06-18)
    • v0.3.0 (2019-05-31)
    • v0.2.1 (2019-05-02)
    • v0.2.0 (2019-04-30)
    • v0.1.0 (2019-04-23)
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