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Features * An open source Java application that you can run from the command line.
* A simple web application.
* A RESTful API.
* Efficiency. The Closure Compiler reduces the size of your JavaScript files and makes them more efficient, helping your application to load faster and reducing your bandwidth needs.
* Code checking. The Closure Compiler provides warnings for illegal JavaScript and warnings for potentially dangerous operations, helping you to produce JavaScript that is less buggy and easier to maintain.
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Features * Below are some examples of analyses that can be run in PLATO and the options that are available to the user. These examples are intended as a jumping off point for the user to customize their own
analyses. For a handy list of all available commands and options, organized by function, see the PLATO Quick Reference, which lists the commands by function and is cross-referenced to their
location in the manual.
* Recode PED/MAP to Binary PLINK format
$ plato load-data --file geno output-bed --file binarygeno
* Recode Binary PLINK to PED/MAP, Only a Single Chromosome $ plato load-data --bfile bingeno --chrom 22 \ output-ped --ped geno.ped --map custom_geno.map
* Perform a Simple Case/Control GWAS (no covariates, Bonferroni corrected p-values)
$ plato load-data --bfile bingeno \
logistic --correction Bonferroni
* PheWAS on Quantitative Outcomes using Markers with MAF between 10% and 40%
$ plato load-data --bfile bingeno \
load-trait --file pheno.txt --missing=”-999” \
filter-maf --min 0.1 --max 0.4
linear --phewas --covariates AGE,BMI
* EWAS (No Genetic Data, Quantitative Predictor Variables) $ plato load-trait --file pheno.txt --dummy-samples --extra-samples
logistic --exclude-markers --use-traits --outcome PHENO
* Concordance Checking (VCF vs. PED/MAP w/o FID) $ plato load-data --vcf-file data.vcf.gz concordance --file geno --no-fid
* GWAS with Dog Data and Permutation Testing $ plato --chroms 38 load-data --file dog_geno logistic --permutations 1000
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LanguagesJava |
LanguagesCPP Java Script |
Source TypeOpen
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Source TypeOpen
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License TypeApache |
License TypeMIT |
OS Type |
OS Type |
Pricing
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