Table 1 An example of the features available in PLATO and other common genomics software

From: PLATO software provides analytic framework for investigating complexity beyond genome-wide association studies

 

PLATO

PLINK4

GCTA59

R/bioconductora

Association analysis

Genome-wide association study

X

X

X

GenABEL60

Environment-wide association study

X

  

PheWAS61

Phenome-wide association study

X

  

PheWAS

Differential CNV burden analysis

X

  

R

Differential gene expression

X

  

ArrayTools62

Gene set enrichment analysis

   

GSEA63

Gene×gene interaction

X

X

 

SNPassoc64

Gene×environment interaction

X

X

X

CGEN65

Differential rare variation analysis

X

  

R, podkat66

Types of statistical tests

Logistic Regression

X

X

 

R

Linear Regression

X

X

 

R

Firth Regression

X

  

GWASTools67

Likelihood ratio test

X

X

 

R

Auto-detect regression type

X

  

GenABEL

Mixed linear model association

  

X

GENESIS68

Family-based association

 

X

 

gap69

Estimation of variance explained

  

X

R

Polygenic modeling

   

gap

Meta-analysis

  

X

gap

Genetic encodings supported

Additive encoding

X

X

X

GenABEL

Dominant encoding

X

X

 

GenABEL

Recessive encoding

X

X

 

GenABEL

Codominant encoding

X

X

 

SNPassoc

Overdominant encoding

   

SNPassoc

Multiple test correction

Bonferroni

X

X

 

R

FDR

X

X

 

R

Permutation

X

X

 

SNPassoc

QC filtering

Marker call rate

X

X

 

SNPRelate57

Sample call rate

X

X

 

SNPRelate

MAF

X

X

X

SNPRelate

LD Pruning

 

X

X

SNPRelate

IBD

 

X

X

SNPRelate

PCA

 

X

X

SNPRelate

  1. aBioconductor is a repository in R that includes many packages. While there may be other packages that perform the same or similar test, we have selected one for illustrative purposes
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