pgxcentre/genipe issues and pull requests

#57 - Support for Impute5 and Shapeit4

Issue - State: open - Opened by Sathish9 about 2 years ago - 1 comment

#56 - genotype rate is lower than before imputation

Issue - State: closed - Opened by AmmyDK over 3 years ago

#55 - Error when --shapeit-extra '--force'

Issue - State: closed - Opened by dgarrimar almost 4 years ago - 2 comments

#54 - Unreleased version of BioPython (1.73) required

Issue - State: closed - Opened by LeoBman almost 6 years ago - 2 comments

#53 - chrX pipeline

Issue - State: closed - Opened by arvkevi almost 6 years ago - 4 comments

#52 - Errors when testing newly installed genipe: TypeError: init() got an unexpected keyword argument 'normalize'

Issue - State: closed - Opened by ashaked almost 7 years ago - 5 comments

#51 - ERROR missing optional module: pyplink

Issue - State: closed - Opened by dlippold almost 7 years ago

#50 - ERROR: Reference and Main panels are not well aligned

Issue - State: closed - Opened by dlippold almost 7 years ago - 1 comment
Labels: wontfix

#49 - Some flaws of the documentation

Issue - State: closed - Opened by dlippold almost 7 years ago

#48 - Error when using a high number of threads for shapeit

Issue - State: closed - Opened by dlippold almost 7 years ago - 19 comments
Labels: wontfix

#47 - Define an option for the directory with the IMPUTE2 reference files

Issue - State: closed - Opened by dlippold almost 7 years ago - 1 comment
Labels: wontfix

#46 - Existing directory 1000GP_Phase3 is not detected

Issue - State: open - Opened by dlippold almost 7 years ago - 1 comment

#45 - Deprecation warning for barh

Issue - State: closed - Opened by lemieuxl almost 7 years ago

#44 - Error with module lifelines, name 'dmatrices' is not defined

Issue - State: closed - Opened by dlippold almost 7 years ago - 3 comments

#43 - Module statsmodels, [... WARNING] interaction term is categorical

Issue - State: closed - Opened by dlippold almost 7 years ago - 1 comment
Labels: wontfix

#42 - Error in file genipe/pipeline/cli.py

Issue - State: closed - Opened by dlippold almost 7 years ago - 2 comments

#41 - Unknown format code 'd' for object of type 'float'

Issue - State: closed - Opened by dlippold almost 7 years ago - 3 comments

#40 - genipe-tutorial fails when broken link

Issue - State: closed - Opened by klevdiamanti over 7 years ago - 2 comments

#39 - options to use bfile instead of impute2 for SKAT?

Issue - State: closed - Opened by gpcr over 7 years ago - 1 comment
Labels: wontfix

#38 - Minor text edits to README

Pull Request - State: closed - Opened by bryketos about 8 years ago - 1 comment

#37 - CoxPH and categorical variables

Issue - State: closed - Opened by lemieuxl over 8 years ago
Labels: bug

#36 - Update documentation

Issue - State: closed - Opened by lemieuxl over 8 years ago
Labels: enhancement

#35 - Optimize MixedLM analysis

Issue - State: closed - Opened by lemieuxl over 8 years ago
Labels: enhancement

#34 - Add basic burden test

Issue - State: open - Opened by legaultmarc over 8 years ago
Labels: new feature

#33 - SKAT - Improve error message when a SNP set is empty

Issue - State: open - Opened by legaultmarc over 8 years ago
Labels: enhancement

#32 - Survival Tutorial: There is a TTE when `event=0`

Issue - State: open - Opened by legaultmarc over 8 years ago
Labels: enhancement, question

#31 - Report R-squared for linear analysis

Issue - State: closed - Opened by lemieuxl over 8 years ago
Labels: enhancement

#30 - Optimize the dosage computation

Issue - State: open - Opened by legaultmarc over 8 years ago
Labels: enhancement

#29 - Sex problem ;-)

Issue - State: closed - Opened by asseling almost 9 years ago
Labels: bug

#28 - Pandas deprecation warning for sort

Issue - State: closed - Opened by lemieuxl almost 9 years ago - 1 comment
Labels: enhancement, wontfix

#27 - Statistical computation fails when no males

Issue - State: closed - Opened by lemieuxl almost 9 years ago
Labels: bug

#26 - Bug when testing only one chromosome

Issue - State: closed - Opened by asseling almost 9 years ago - 1 comment
Labels: bug

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

Issue - State: closed - Opened by lemieuxl almost 9 years ago
Labels: bug

#24 - Add a check for the drmaa module

Issue - State: closed - Opened by lemieuxl almost 9 years ago - 1 comment
Labels: enhancement

#23 - Add the "BED" format for extraction

Issue - State: closed - Opened by lemieuxl almost 9 years ago - 1 comment
Labels: enhancement

#22 - Add a way to skip finding exclusions if it was already performed

Issue - State: closed - Opened by lemieuxl almost 9 years ago
Labels: enhancement

#21 - Get chromosome length from legend file

Issue - State: closed - Opened by lemieuxl almost 9 years ago
Labels: enhancement

#20 - Add chromosome X imputation in the pipeline

Issue - State: closed - Opened by lemieuxl almost 9 years ago
Labels: enhancement

#19 - Add the "lgen" format for extraction

Issue - State: closed - Opened by lemieuxl about 9 years ago - 1 comment
Labels: enhancement

#18 - More options to change Shapeit parameters

Issue - State: closed - Opened by lemieuxl about 9 years ago - 1 comment
Labels: enhancement

#17 - More options to change Impute2 parameters

Issue - State: closed - Opened by lemieuxl about 9 years ago - 1 comment
Labels: enhancement

#16 - MixedLM - Failed test

Issue - State: closed - Opened by lemieuxl about 9 years ago
Labels: bug

#15 - Exception raised when start or end time is None

Issue - State: closed - Opened by lemieuxl about 9 years ago
Labels: bug

#14 - Too many client events (DRMAA)

Issue - State: closed - Opened by lemieuxl about 9 years ago
Labels: bug

#13 - There is no Q value for SKAT-O

Issue - State: closed - Opened by legaultmarc over 9 years ago
Labels: bug

#12 - Multiple phenotypes

Issue - State: closed - Opened by legaultmarc over 9 years ago - 1 comment
Labels: enhancement

#11 - Windows compatibility for paths in the tests module

Issue - State: closed - Opened by legaultmarc over 9 years ago - 1 comment
Labels: bug

#10 - Bug in multiprocessing on Mac OS

Issue - State: closed - Opened by legaultmarc over 9 years ago
Labels: bug, wontfix

#9 - Perform initial strand check using reference genome

Issue - State: closed - Opened by lemieuxl over 9 years ago - 1 comment
Labels: enhancement