Limix’s documentation

Table of contents

• Install
  • Pip
  • Conda
• I/O module
  • BIMBAM
  • BGEN reader
  • CSV reader
  • HDF5 reader
  • NumPy reader
  • PLINK reader
• Quality control
  • Box-Cox
  • Dependent columns
  • Genotype
  • Impute
  • Kinship
  • Normalisation
• Quantitative trait locus
  • Introduction
  • Statistical test
  • Single-trait association
  • Non-normal trait association
  • Single-trait with interaction
  • Multi-trait association
• Variance decomposition
  • Single-trait decomposition
• Heritability estimation
• Plotting
  • Kinship
  • Manhattan
  • Quantile-quantile plot
• Command line interface
  • Introduction
  • Kinship
  • Plink BED format
  • BIMBAM file formats
  • HDF5
  • CSV
  • Image
  • GWAS
• Statistics
  • Alleles
  • Chi-square mixture
  • Ground truth evaluation
  • Kinship
  • Likelihood-ratio test
  • Principal component analysis
  • P-value correction
• Model
  • Linear Mixed Models
  • Generalised Linear Mixed Models
  • Gaussian Process
  • Generalised Gaussian Process
  • Covariance
  • Mean
• API reference
  • I/O module
  • Quality control
  • Statistics
  • Heritability estimation
  • Variance decomposition
  • Quantitative trait loci
  • Plotting & Graphics
  • Shell utilities

Comments and bugs

You can get the source and open issues on Github.