danielseaton/corrall

Issues

• Integrate with output from cellSNP (as another option compared to GATK ASEReadCounter)

  #13 opened 5 years ago by danielseaton
  0

• Handling "chr#" vs "#" formats of chromosomes

  #12 opened 5 years ago by danielseaton
  0

• Filter SNPs to quantify ASE for based on donor genotype, not ASE counts

  #11 opened 5 years ago by danielseaton
  0

• separate chrB count file merging from phasing to eQTL SNP functionality

  #9 opened 6 years ago by danielseaton
  0

• allow option of outputting ASE fractions or counts after phasing relative to eQTL SNPs

  #10 opened 6 years ago by danielseaton
  0

• phase ASE across cells from multiple donors, using a reference SNP

  #4 opened 6 years ago by danielseaton
  0

• Regression tests for linear models

  #7 opened 6 years ago by danielseaton
  1

• Move linear model code to a module

  #6 opened 6 years ago by danielseaton
  1

• Convert linear models to LIMIX, including GLMMs, with random effects and covariates

  #8 opened 6 years ago by danielseaton
  0

• Take input from alternative ASE quantification pipelines

  #5 opened 6 years ago by danielseaton
  0

• tests for vcf_utils

  #3 opened 6 years ago by danielseaton
  0

• Use input table with file locations for aggregate_data_by_donor

  #2 opened 6 years ago by danielseaton
  0

• Check SNP ID, not just position, when querying in vcf_utils.py

  #1 opened 7 years ago by danielseaton
  0