All modules for which code is available

• pyGenClean
• pyGenClean.Contamination.contamination
• pyGenClean.DupSNPs.duplicated_snps
• pyGenClean.DupSamples.duplicated_samples
• pyGenClean.Ethnicity.check_ethnicity
• pyGenClean.Ethnicity.find_outliers
• pyGenClean.Ethnicity.plot_eigenvalues
• pyGenClean.FlagHW.flag_hw
• pyGenClean.FlagMAF.flag_maf_zero
• pyGenClean.HeteroHap.remove_heterozygous_haploid
• pyGenClean.LaTeX.auto_report
• pyGenClean.LaTeX.merge_reports
• pyGenClean.LaTeX.utils
• pyGenClean.MarkerMissingness.snp_missingness
• pyGenClean.Misc.compare_gold_standard
• pyGenClean.NoCallHetero.clean_noCall_hetero_snps
• pyGenClean.NoCallHetero.heterozygosity_plot
• pyGenClean.PlateBias.plate_bias
• pyGenClean.PlinkUtils
• pyGenClean.PlinkUtils.compare_bim
• pyGenClean.PlinkUtils.plot_MDS
• pyGenClean.PlinkUtils.plot_MDS_standalone
• pyGenClean.PlinkUtils.subset_data
• pyGenClean.RelatedSamples.find_related_samples
• pyGenClean.RelatedSamples.merge_related_samples
• pyGenClean.SampleMissingness.sample_missingness
• pyGenClean.SexCheck.baf_lrr_plot
• pyGenClean.SexCheck.gender_plot
• pyGenClean.SexCheck.sex_check
• pyGenClean.pipeline_error
• pyGenClean.run_data_clean_up