Recent entries:
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Filtering GWAS 0.05 results
| tags: [ Data Cleaning GWAS R ] categories: [ Coding ]
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GWAS rerun MAF 0.05
| tags: [ Gaston GWAS R ] categories: [ Coding Experiments ]
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Using variants unfiltered for MAF for PCA and heritability analysis
| tags: [ Data Cleaning Genomic Data Heritability PCA ] categories: [ Coding Experiments ]
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Re-estimating heritability of traits - GCTA
| tags: [ GCTA Heritability ] categories: [ Coding Experiments Reading ]
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Excluding low frequency variants and genomic PCA
| tags: [ Data Cleaning PCA PLINK ] categories: [ Coding Experiments ]
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Generating beta-values for significant SNPs
| tags: [ Gaston Genomic Data GWAS Heritability ] categories: [ Coding ]
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Filtering GWAS (w/ covariates) results
| tags: [ Gaston Genomic Data GWAS Heritability ] categories: [ Coding Experiments ]
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Adding age and sex as covariates
| tags: [ Gaston GCTA Genomic Data GREML Heritability ] categories: [ Coding Experiments ]
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SNP heritability
| tags: [ Gaston GCTA Genomic Data GWAS Heritability MLMA ] categories: [ Experiments Coding ]
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Annotating signficant GWAS hits
| tags: [ Genomic Data GWAS ] categories: [ Coding Experiments ]
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Performing GWAS on heritable traits
| tags: [ Gaston GCTA Genomic Data GWAS Heritability ] categories: [ Coding Experiments ]
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MLMA GWAS for most heritable trait
| tags: [ GCTA Genomic Data GWAS MLMA GREML Linux ] categories: [ Coding Experiments ]
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Estimating heritability of principal components using GCTA
| tags: [ GCTA Genomic Data Heritability ] categories: [ Coding Experiments ]
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Trying GCTA to perform heritability analysis
| tags: [ GCTA Genomic Data Heritability Linux ] categories: [ Coding Experiments ]
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Including principal components for estimating heritability
| tags: [ Gaston Genomic Data Heritability ] categories: [ Coding Experiments ]
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Using gaston for estimating heritability-1
| tags: [ Gaston Genomic Data R PLINK Heritability ] categories: [ Coding Experiments ]
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Trying gaston to generate genetic relationship matrix
| tags: [ Genomic Data Gaston ] categories: [ Coding Experiments ]
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Performing PCA on filtered NIES genomic data
| tags: [ Genomic Data PCA PLINK ] categories: [ Coding Experiments ]
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Re-trying default merge
| tags: [ Data Cleaning Genomic Data PLINK R ] categories: [ Coding Experiments ]
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Troubleshooting missing genotype filtering
| tags: [ Data Cleaning Genomic Data PLINK R ] categories: [ Coding Experiments ]
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Performing PCA on genomic data
| tags: [ Genomic Data Linux PCA PLINK R ] categories: [ Coding Experiments ]
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Generating stats for merged data and extracting data for NIES
| tags: [ Data Cleaning Genomic Data Linux PLINK ] categories: [ Coding Experiments ]
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Fixing WGS ID and merging data
| tags: [ Data Cleaning Genomic Data Linux PLINK R ] categories: [ Coding Experiments ]
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Extracting data for variants common in both file sets
| tags: [ Data Cleaning Genomic Data Linux PLINK R ] categories: [ Coding Experiments ]
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Generating basic statistics for final genomic data sets
| tags: [ Data Cleaning Genomic Data Linux PLINK ] categories: [ Coding Experiments ]
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Converting SNP array data
| tags: [ Genomic Data PLINK ] categories: [ Coding Experiments ]
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Merging genomic data sets
| tags: [ Data Cleaning Genomic Data Linux PLINK ] categories: [ Coding Experiments ]
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Cleaning and preparing genomic data
| tags: [ Data Cleaning Genomic Data Linux PLINK R ] categories: [ Coding Experiments ]
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Extracting genomic data exclusive to NIES
| tags: [ Genomic Data Data Cleaning Linux PLINK R ] categories: [ Coding Experiments ]
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Generating basic statistics for merged data set
| tags: [ Genomic Data Linux PLINK R ] categories: [ Coding Experiments ]
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Extracting common variants from both data sets
| tags: [ Data Cleaning Genomic Data Linux PLINK PCA R ] categories: [ Coding Experiments ]
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Generating basic statistics for genomic data sets
| tags: [ Genomic Data Linux PLINK ] categories: [ Coding Experiments ]
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Trying bmerge function
| tags: [ Genomic Data Linux PLINK ] categories: [ Coding Experiments ]
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Getting started with PLINK
| tags: [ Linux PLINK Genomic Data ] categories: [ Coding ]
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PCA of Phenotypic Data
| tags: [ PCA Ocular Biometry R ] categories: [ Coding Experiments ]
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Adding Conjunctival UVAF to dataset
| tags: [ Bivariate Correlations Data Cleaning Imputation Ocular Biometry PCA R ] categories: [ Coding Experiments ]
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Pearson's correlations on imputed data set
| tags: [ Data Cleaning Imputation Bivariate Correlations R ] categories: [ Coding Experiments ]
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MIPCA of Phenotypic Data without LogMAR-with-PH values
| tags: [ Data Cleaning Imputation PCA R ] categories: [ Coding Experiments ]
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Multiple PCA Imputation of Quantitative Phenotypic Data - updated
| tags: [ Data Cleaning Imputation PCA R ] categories: [ Coding Experiments ]
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Multiple PCA Imputation of Phenotypic Data
| tags: [ R Imputation PCA ] categories: [ Coding Experiments ]
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Example of data imputation with missMDA
| tags: [ Data Cleaning Imputation PCA R ] categories: [ Experiments Coding ]
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Understanding PCA
| tags: [ PCA Imputation Data Cleaning ] categories: [ Reading ]
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Subsetting relevant phenotypic data
| tags: [ Data Cleaning R ] categories: [ Coding ]
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Understanding ocular biometric measurements
| tags: [ Reading Ocular Biometry ] categories: [ Reading ]
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Finding outliers in quantitative data
| tags: [ Data Cleaning R ] categories: [ Coding Experiments ]
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Plotting histograms for quantitative phenotypic data
| tags: [ R Data Cleaning ] categories: [ Coding ]
- Cleaning phenotypic data