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  • 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

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