Issues

• Replace "sex chromosome" by more accurate "X chromosome"

  task
  AlphaGenes/AlphaPeel#296 · Filter by author XingerTang opened on Aug 18, 2026
  

• Check input formats

  discussion
  AlphaGenes/AlphaPeel#294 · Filter by author XingerTang opened on Jul 29, 2026
  

• Phenotype penetrance probability error handling

  task
  AlphaGenes/AlphaPeel#290 · Filter by author RosCraddock opened on Jun 30, 2026
  1

• Enable geno_error and seq_error input that allows variation across loci

  task
  AlphaGenes/AlphaPeel#284 · Filter by author XingerTang opened on Jun 17, 2026
  

• Phased haplotype input

  discussion
  AlphaGenes/AlphaPeel#281 · Filter by author XingerTang opened on Jun 11, 2026
  

• Add support for X chromosome input in haplotypes

  task
  AlphaGenes/AlphaPeel#279 · Filter by author XingerTang opened on Jun 4, 2026
  

• Reading previous imputation results and proceed with new data

  discussion
  AlphaGenes/AlphaPeel#274 · Filter by author XingerTang opened on May 28, 2026
  

• Check calculation of allele frequency for X chromosome

  task
  AlphaGenes/AlphaPeel#265 · Filter by author gregorgorjanc opened on May 20, 2026
  8

  

• Redesign hybrid accuracy test

  discussion
  AlphaGenes/AlphaPeel#258 · Filter by author XingerTang opened on May 15, 2026
  2

  

• Fixing part of AlphaGenes/AlphaPeel#227 Pt.3

  task
  AlphaGenes/AlphaPeel#248 · Filter by author XingerTang opened on Apr 20, 2026
  

• Fixing part of AlphaGenes/AlphaPeel#227 Pt.2

  task
  AlphaGenes/AlphaPeel#247 · Filter by author XingerTang opened on Apr 20, 2026
  

• Consolidate the docs usage section with tools such as sphinx-argparse-cli

  discussion
  AlphaGenes/AlphaPeel#245 · Filter by author XingerTang opened on Apr 17, 2026
  

• Continuous age of onset in phenotype penetrance probabilities

  task
  AlphaGenes/AlphaPeel#235 · Filter by author RosCraddock opened on Mar 19, 2026
  1

  

• Add an image/scheme of autosomal, X, Y, and mt to the docs

  discussiondocumentation
  Feature

  AlphaGenes/AlphaPeel#232 · Filter by author gregorgorjanc opened on Mar 18, 2026
  1

  

• Summary of TODO tasks in AlphaGenes/AlphaPeel#219 discussion

  discussion
  AlphaGenes/AlphaPeel#227 · Filter by author XingerTang opened on Mar 5, 2026
  2

  

• Add -pheno output and -pheno_threshold

  AlphaGenes/AlphaPeel#218 · Filter by author RosCraddock opened on Feb 12, 2026
  

• Mismatch between haplotype output and genotype output

  AlphaGenes/AlphaPeel#211 · Filter by author XingerTang opened on Jan 29, 2026
  1

  

• Calculate accuracy metrics by sex

  enhancement
  AlphaGenes/AlphaPeel#203 · Filter by author gregorgorjanc opened on Dec 18, 2025
  

• x_chr example showing the needed improvements

  insights
  AlphaGenes/AlphaPeel#199 · Filter by author AprilYUZhang opened on Nov 9, 2025
  11

  

• One phenotype to multi-locus genotype

  insights
  AlphaGenes/AlphaPeel#197 · Filter by author RosCraddock opened on Oct 29, 2025
  

• Add support for Y chromosome imputation

  insights
  AlphaGenes/AlphaPeel#194 · Filter by author gregorgorjanc opened on Sep 25, 2025
  

• There is one fixed error value in Peeling.py that should be parameter

  insights
  AlphaGenes/AlphaPeel#193 · Filter by author gregorgorjanc opened on May 15, 2025
  6

  

• Review functional tests for specific errors

  insightstests
  AlphaGenes/AlphaPeel#178 · Filter by author RosCraddock opened on Oct 14, 2024
  1

  

• Review Accuracy Test Outputs

  insights
  AlphaGenes/AlphaPeel#172 · Filter by author RosCraddock opened on Aug 22, 2024
  2

  

• Add seed value input to the tests

  insights
  AlphaGenes/AlphaPeel#170 · Filter by author XingerTang opened on Aug 19, 2024
  5