gymrek-lab/happler issues and pull requests

#42 - feat: flexible snp branching

Pull Request - State: closed - Opened by aryarm over 1 year ago

#41 - refactor: split finemap and susie into different rules

Pull Request - State: closed - Opened by aryarm over 1 year ago

#40 - refactor: split pipeline into subworkflows

Pull Request - State: closed - Opened by aryarm over 1 year ago

#39 - feat: covariates

Pull Request - State: closed - Opened by aryarm almost 2 years ago

#38 - fix: bug with precision and ordering of phenotypes and enable CKD analysis

Pull Request - State: closed - Opened by aryarm almost 2 years ago

#37 - rank alleles by their t scores instead of their pvalues

Issue - State: closed - Opened by aryarm about 2 years ago - 1 comment

#36 - feat: run happler within the simulation pipeline

Pull Request - State: closed - Opened by aryarm about 2 years ago

#35 - feat: GitHub actions

Pull Request - State: closed - Opened by aryarm over 2 years ago

#34 - just a quick update

Pull Request - State: closed - Opened by aryarm over 2 years ago

#33 - implement parameter testing in the simulation framework

Issue - State: open - Opened by aryarm over 3 years ago
Labels: enhancement

#33 - implement parameter testing in the simulation framework

Issue - State: open - Opened by aryarm over 3 years ago
Labels: enhancement

#33 - implement parameter testing in the simulation framework

Issue - State: open - Opened by aryarm over 3 years ago
Labels: enhancement

#32 - rerun simulations multiple times and combine results to create simulation scores

Issue - State: open - Opened by aryarm over 3 years ago
Labels: enhancement

#32 - rerun simulations multiple times and combine results to create simulation scores

Issue - State: open - Opened by aryarm over 3 years ago
Labels: enhancement

#32 - rerun simulations multiple times and combine results to create simulation scores

Issue - State: open - Opened by aryarm over 3 years ago
Labels: enhancement

#31 - refactor for FINEMAP and SuSiE execution

Issue - State: closed - Opened by aryarm over 3 years ago
Labels: refactor

#30 - not responding to ctrl+c

Issue - State: open - Opened by aryarm almost 3 years ago

#29 - try to force docs rebuild

Pull Request - State: closed - Opened by aryarm almost 3 years ago

#28 - add delta bic backend and update poetry instructions

Pull Request - State: closed - Opened by aryarm almost 3 years ago

#27 - wip: UKB simulations and new tree termination backend

Pull Request - State: closed - Opened by aryarm almost 3 years ago

#26 - pass two_snps_perfect tests

Pull Request - State: closed - Opened by aryarm almost 3 years ago

#25 - consider pruning children of the root

Issue - State: open - Opened by aryarm almost 3 years ago

#24 - pre-sort haplotypes in Haplotype.node_indices

Issue - State: open - Opened by aryarm almost 3 years ago

#23 - come up with a better way of encoding alleles in the tree

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

#22 - fix alleles in haplotype output file

Issue - State: closed - Opened by aryarm almost 3 years ago - 1 comment

#21 - handle edge cases revealed by example tests

Pull Request - State: closed - Opened by aryarm almost 3 years ago

#21 - handle edge cases revealed by example tests

Pull Request - State: closed - Opened by aryarm almost 3 years ago

#20 - create more example tests and add tree termination tests

Pull Request - State: closed - Opened by aryarm about 3 years ago

#20 - create more example tests and add tree termination tests

Pull Request - State: closed - Opened by aryarm about 3 years ago

#20 - create more example tests and add tree termination tests

Pull Request - State: closed - Opened by aryarm about 3 years ago

#19 - create example tests and write to new `.haps` output format

Pull Request - State: closed - Opened by aryarm about 3 years ago

#18 - finish initial method draft and create test cases

Pull Request - State: closed - Opened by aryarm about 3 years ago

#17 - use a static type checker

Issue - State: open - Opened by aryarm about 3 years ago

#16 - type-hinting numpy mixed array records

Issue - State: open - Opened by aryarm about 3 years ago

#16 - type-hinting numpy mixed array records

Issue - State: open - Opened by aryarm about 3 years ago

#16 - type-hinting numpy mixed array records

Issue - State: open - Opened by aryarm about 3 years ago

#15 - finish initial draft of TreeBuilder class

Pull Request - State: closed - Opened by aryarm about 3 years ago

#15 - finish initial draft of TreeBuilder class

Pull Request - State: closed - Opened by aryarm about 3 years ago

#15 - finish initial draft of TreeBuilder class

Pull Request - State: closed - Opened by aryarm about 3 years ago

#14 - create classes for handling haplotypes

Pull Request - State: closed - Opened by aryarm about 3 years ago

#14 - create classes for handling haplotypes

Pull Request - State: closed - Opened by aryarm about 3 years ago

#14 - create classes for handling haplotypes

Pull Request - State: closed - Opened by aryarm about 3 years ago

#13 - start on tree and treebuilder

Pull Request - State: closed - Opened by aryarm about 3 years ago

#13 - start on tree and treebuilder

Pull Request - State: closed - Opened by aryarm about 3 years ago

#12 - create a method for converting the tree to ascii

Issue - State: closed - Opened by aryarm about 3 years ago - 1 comment
Labels: enhancement

#12 - create a method for converting the tree to ascii

Issue - State: closed - Opened by aryarm about 3 years ago - 1 comment
Labels: enhancement

#12 - create a method for converting the tree to ascii

Issue - State: closed - Opened by aryarm about 3 years ago - 1 comment
Labels: enhancement

#11 - try to use rtd_poetry

Pull Request - State: closed - Opened by aryarm about 3 years ago

#11 - try to use rtd_poetry

Pull Request - State: closed - Opened by aryarm about 3 years ago

#10 - use poetry v1.2+

Issue - State: closed - Opened by aryarm about 3 years ago - 1 comment

#9 - an output file format

Issue - State: closed - Opened by aryarm about 3 years ago - 4 comments

#9 - an output file format

Issue - State: closed - Opened by aryarm about 3 years ago - 4 comments

#9 - an output file format

Issue - State: closed - Opened by aryarm about 3 years ago - 4 comments

#8 - create a TreeBuilder class

Issue - State: closed - Opened by aryarm about 3 years ago

#8 - create a TreeBuilder class

Issue - State: closed - Opened by aryarm about 3 years ago

#8 - create a TreeBuilder class

Issue - State: closed - Opened by aryarm about 3 years ago

#7 - wip: data module

Pull Request - State: closed - Opened by aryarm about 3 years ago

#7 - wip: data module

Pull Request - State: closed - Opened by aryarm about 3 years ago

#7 - wip: data module

Pull Request - State: closed - Opened by aryarm about 3 years ago

#6 - support for STRs in the Genotypes class

Issue - State: closed - Opened by aryarm about 3 years ago - 3 comments
Labels: enhancement

#5 - allow for filtering by AAF in Genotypes class

Issue - State: closed - Opened by aryarm about 3 years ago
Labels: enhancement

#5 - allow for filtering by AAF in Genotypes class

Issue - State: closed - Opened by aryarm about 3 years ago
Labels: enhancement

#5 - allow for filtering by AAF in Genotypes class

Issue - State: closed - Opened by aryarm about 3 years ago
Labels: enhancement

#5 - allow for filtering by AAF in Genotypes class

Issue - State: closed - Opened by aryarm about 3 years ago
Labels: enhancement

#4 - create a Data module

Pull Request - State: closed - Opened by aryarm about 3 years ago

#4 - create a Data module

Pull Request - State: closed - Opened by aryarm about 3 years ago

#4 - create a Data module

Pull Request - State: closed - Opened by aryarm about 3 years ago

#3 - add a `--range` parameter to the cli

Issue - State: closed - Opened by aryarm about 3 years ago - 1 comment
Labels: enhancement

#3 - add a `--range` parameter to the cli

Issue - State: closed - Opened by aryarm about 3 years ago - 1 comment
Labels: enhancement

#3 - add a `--range` parameter to the cli

Issue - State: closed - Opened by aryarm about 3 years ago - 1 comment
Labels: enhancement

#2 - setup project

Pull Request - State: closed - Opened by aryarm about 3 years ago

#1 - support for PLINK2-type file formats

Issue - State: closed - Opened by aryarm over 3 years ago - 1 comment
Labels: enhancement

#1 - support for PLINK2-type file formats

Issue - State: closed - Opened by aryarm over 3 years ago - 1 comment
Labels: enhancement

#1 - support for PLINK2-type file formats

Issue - State: closed - Opened by aryarm over 3 years ago - 1 comment
Labels: enhancement

GitHub / gymrek-lab/happler issues and pull requests