pgxcentre/genipe

Issues

• Support for Impute5 and Shapeit4

  #57 opened 3 years ago by Sathish9
  1

• Error when using a high number of threads for shapeit

  #48 opened 7 years ago by dlippold
  19

• genotype rate is lower than before imputation

  #56 opened 4 years ago by AmmyDK
  0

• Error with module lifelines, name 'dmatrices' is not defined

  #44 opened 7 years ago by dlippold
  3

• chrX pipeline

  #53 opened 6 years ago by arvkevi
  4

• Error when --shapeit-extra '--force'

  #55 opened 4 years ago by dgarrimar
  2

• Unreleased version of BioPython (1.73) required

  #54 opened 6 years ago by LeoBman
  2

• Errors when testing newly installed genipe: TypeError: __init__() got an unexpected keyword argument 'normalize'

  #52 opened 7 years ago by ashaked
  5

• ERROR missing optional module: pyplink

  #51 opened 7 years ago by dlippold
  0

• Error in file genipe/pipeline/cli.py

  #42 opened 7 years ago by dlippold
  2

• Windows compatibility for paths in the tests module

  #11 opened 7 years ago by legaultmarc
  1

• Deprecation warning for barh

  #45 opened 7 years ago by lemieuxl
  0

• Some flaws of the documentation

  #49 opened 7 years ago by dlippold
  0

• Unknown format code 'd' for object of type 'float'

  #41 opened 7 years ago by dlippold
  3

• ERROR: Reference and Main panels are not well aligned

  #50 opened 7 years ago by dlippold
  1

• Define an option for the directory with the IMPUTE2 reference files

  #47 opened 7 years ago by dlippold
  1

• Existing directory 1000GP_Phase3 is not detected

  #46 opened 7 years ago by dlippold
  1

• Module statsmodels, [... WARNING] interaction term is categorical

  #43 opened 7 years ago by dlippold
  1

• genipe-tutorial fails when broken link

  #40 opened 8 years ago by klevdiamanti
  2

• options to use bfile instead of impute2 for SKAT?

  #39 opened 8 years ago by gpcr
  1

• Update documentation

  #36 opened 9 years ago by lemieuxl
  0

• CoxPH and categorical variables

  #37 opened 9 years ago by lemieuxl
  0

• Add a way to skip finding exclusions if it was already performed

  #22 opened 9 years ago by lemieuxl
  0

• Pandas deprecation warning for sort

  #28 opened 9 years ago by lemieuxl
  1

• Optimize MixedLM analysis

  #35 opened 9 years ago by lemieuxl
  0

• Add basic burden test

  #34 opened 9 years ago by legaultmarc
  0

• More options to change Impute2 parameters

  #17 opened 9 years ago by lemieuxl
  1

• More options to change Shapeit parameters

  #18 opened 9 years ago by lemieuxl
  1

• Add a check for the drmaa module

  #24 opened 9 years ago by lemieuxl
  1

• Add the "BED" format for extraction

  #23 opened 9 years ago by lemieuxl
  1

• Add the "lgen" format for extraction

  #19 opened 9 years ago by lemieuxl
  1

• Optimize the dosage computation

  #30 opened 9 years ago by legaultmarc
  0

• SKAT - Improve error message when a SNP set is empty

  #33 opened 9 years ago by legaultmarc
  0

• Survival Tutorial: There is a TTE when `event=0`

  #32 opened 9 years ago by legaultmarc
  0

• Report R-squared for linear analysis

  #31 opened 9 years ago by lemieuxl
  0

• Chromosome 25 (PAR1 and PAR2) should be skipped if no markers available

  #25 opened 9 years ago by lemieuxl
  0

• Sex problem ;-)

  #29 opened 9 years ago by asseling
  0

• Statistical computation fails when no males

  #27 opened 9 years ago by lemieuxl
  0

• Bug when testing only one chromosome

  #26 opened 9 years ago by asseling
  1

• Subset of chromosomes

  #7 opened 9 years ago by lemieuxl
  0

• Add chromosome X imputation in the pipeline

  #20 opened 9 years ago by lemieuxl
  0

• Get chromosome length from legend file

  #21 opened 9 years ago by lemieuxl
  0

• Multiple phenotypes

  #12 opened 9 years ago by legaultmarc
  1

• MixedLM - Failed test

  #16 opened 9 years ago by lemieuxl
  0

• Too many client events (DRMAA)

  #14 opened 10 years ago by lemieuxl
  0

• Exception raised when start or end time is None

  #15 opened 10 years ago by lemieuxl
  0

• There is no Q value for SKAT-O

  #13 opened 10 years ago by legaultmarc
  0

• Statistical analysis on imputed genotypes (dosage)

  #8 opened 10 years ago by lemieuxl
  1

• Perform initial strand check using reference genome

  #9 opened 10 years ago by lemieuxl
  1

• Bug in multiprocessing on Mac OS

  #10 opened 10 years ago by legaultmarc
  0