Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / UW-GAC/GENESIS issues and pull requests
#115 - covariance between the main effect (SNP) and the interaction effect
Issue -
State: open - Opened by lissettegomez 16 days ago
- 1 comment
#114 - Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : object 'saddle' not found
Issue -
State: closed - Opened by ruuhsu 2 months ago
- 3 comments
#113 - Available rare variant aggregate association tests
Issue -
State: closed - Opened by CristianRiccio 2 months ago
- 1 comment
#112 - Filter extremely small p-values by setting them to Machine$double.xmin
Pull Request -
State: closed - Opened by amstilp 7 months ago
#111 - Add a helper function to calculate and filter pchisq values
Pull Request -
State: closed - Opened by amstilp 7 months ago
- 1 comment
#110 - Filter extreme p-values using `.Machine$double.xmin`
Issue -
State: open - Opened by amstilp 7 months ago
- 1 comment
#109 - Cholesky factorization failed
Issue -
State: open - Opened by wangfan860 7 months ago
- 1 comment
#108 - pcrelate: error with rbindlist()
Issue -
State: open - Opened by AmandaHWChong 8 months ago
- 1 comment
#107 - Issue: Running PCAir on 140K individuals
Issue -
State: closed - Opened by AmandaHWChong 9 months ago
- 1 comment
#106 - Issue with PCAir - Segmentation fault (core dumped)
Issue -
State: closed - Opened by AmandaHWChong 9 months ago
- 1 comment
#105 - Error using assocTestAggregate
Issue -
State: open - Opened by pjuge 11 months ago
- 1 comment
#104 - HOW to FIX - PCAir excludes all my SNPs because there is no chromosome information
Issue -
State: closed - Opened by GabryS3 11 months ago
- 1 comment
#103 - Conditional analysis
Issue -
State: closed - Opened by angelosarmen 11 months ago
- 1 comment
#102 - High Memory Consumption with Large Dataset in PC-Relate
Issue -
State: open - Opened by ecyeh about 1 year ago
- 1 comment
#101 - Error when running the pcrelate function
Issue -
State: closed - Opened by AmandaHWChong over 1 year ago
- 3 comments
#100 - ERROR:unused arguments (two.stage = TRUE, norm.option = "all", rescale = "residSD")
Issue -
State: closed - Opened by DamienTan over 1 year ago
- 2 comments
#99 - analysis pipeline for chromosome X
Issue -
State: closed - Opened by candicecjj over 1 year ago
- 1 comment
#98 - pcrelate REDUCE error while calculating individual AF betas
Issue -
State: closed - Opened by BEFH about 2 years ago
- 8 comments
#97 - add check in varCompCI that family is gaussian
Issue -
State: open - Opened by smgogarten about 2 years ago
#96 - Estimate PVE
Issue -
State: closed - Opened by MARCPUCV about 2 years ago
- 1 comment
#95 - correctK2() drops samples under specific conditions
Issue -
State: open - Opened by broomej about 2 years ago
- 1 comment
#94 - enable returning the covariance matrix for GxE tests
Pull Request -
State: open - Opened by mconomos over 2 years ago
- 1 comment
#93 - Add burden test values to SMMAT output
Pull Request -
State: closed - Opened by amstilp over 2 years ago
- 2 comments
#92 - Error in seqVCF2GDS(vcf.files, gds.file, verbose = FALSE)
Issue -
State: closed - Opened by Bulouere over 2 years ago
- 1 comment
#91 - fitNullModel doesn't converge when provided a list of matrices with more than 1 matrix
Issue -
State: open - Opened by tamartsi over 2 years ago
- 3 comments
#90 - add fastSMMAT option and document
Pull Request -
State: closed - Opened by mconomos over 2 years ago
- 1 comment
#89 - bug fix for pcrelate with multiple cores
Pull Request -
State: closed - Opened by smgogarten over 2 years ago
#88 - pcrelateToMatrix slow on 50k samples
Issue -
State: closed - Opened by byoo over 2 years ago
- 10 comments
#87 - Error in assocTestSingle() results when covariate is confounded with SNP genotype.
Issue -
State: open - Opened by rmsegnitz over 2 years ago
- 6 comments
#86 - `fitted.values` in non-mixed null models are not what we expect
Issue -
State: open - Opened by amstilp over 2 years ago
#85 - Fix bug with SPA p-values for glm models
Pull Request -
State: closed - Opened by amstilp over 2 years ago
- 2 comments
#84 - SPA association tests are incorrect for non-mixed models
Issue -
State: closed - Opened by amstilp over 2 years ago
- 1 comment
Labels: bug
#83 - bug fix: makeSparseMatrix handles numeric sample IDs
Pull Request -
State: closed - Opened by smgogarten over 2 years ago
#82 - errors trying to use makeSparseMatrix
Issue -
State: closed - Opened by earosenthal over 2 years ago
- 5 comments
#81 - replace travis build with github actions
Pull Request -
State: closed - Opened by smgogarten over 2 years ago
#80 - Adding functions to perform meta-analysis
Issue -
State: open - Opened by marcora almost 3 years ago
- 2 comments
#79 - Confusing error message in `assocTestSingle` when samples in null model are not in GDS file
Issue -
State: closed - Opened by amstilp almost 3 years ago
#78 - Subset covariance matrix to samples in sample.id if specified
Pull Request -
State: closed - Opened by amstilp almost 3 years ago
- 4 comments
#77 - Error in assocTestSingle with Score.SPA test
Issue -
State: closed - Opened by ZeyuanSong about 3 years ago
- 3 comments
#76 - functions for meta analysis
Pull Request -
State: open - Opened by mconomos about 3 years ago
#75 - recessive and dominant coding
Pull Request -
State: closed - Opened by smgogarten about 3 years ago
- 2 comments
#74 - fitnullmodel error for matrix with negatives
Issue -
State: closed - Opened by Reavyr about 3 years ago
- 3 comments
#73 - Outdated pcair() call in vignette
Issue -
State: closed - Opened by pamelarussell about 3 years ago
- 2 comments
#72 - Parallel subfn
Pull Request -
State: closed - Opened by smgogarten about 3 years ago
#71 - Parallel
Pull Request -
State: closed - Opened by smgogarten about 3 years ago
- 3 comments
#70 - pcrelate issue for large sample size
Issue -
State: closed - Opened by GraceSheng about 3 years ago
- 4 comments
#69 - assocTestSingle exhausts iterators
Issue -
State: closed - Opened by kaskarn over 3 years ago
- 1 comment
#68 - meanImpute calculation is split into blocks for large matrices
Pull Request -
State: closed - Opened by smgogarten over 3 years ago
- 1 comment
#67 - Generate Dense Kinship matrix
Issue -
State: closed - Opened by nkurniansyah over 3 years ago
- 1 comment
#66 - Error in if (any(i < 0L)) { : missing value where TRUE/FALSE needed
Issue -
State: closed - Opened by vkp3 over 3 years ago
- 7 comments
#65 - updated code for recessive coding to test in association tests
Pull Request -
State: closed - Opened by mchughc over 3 years ago
- 1 comment
#64 - Max Number of samples for PC-AIR
Issue -
State: closed - Opened by jjfarrell over 3 years ago
- 13 comments
#63 - Vsif
Pull Request -
State: closed - Opened by smgogarten over 3 years ago
- 3 comments
#62 - variant-specific inflation factors branch
Pull Request -
State: closed - Opened by tamartsi over 3 years ago
- 1 comment
#61 - Issue with GxE interaction with Score test in assocTestSingle
Issue -
State: closed - Opened by d1eone over 3 years ago
- 1 comment
#60 - assocTestSingle results: MAC, n.obs and freq don't match.
Issue -
State: closed - Opened by yangli-ai almost 4 years ago
- 4 comments
#59 - Var approx v2
Pull Request -
State: closed - Opened by mconomos almost 4 years ago
#58 - change use of apply in makeSparseMatrix to GENESIS:::.apply
Issue -
State: closed - Opened by mchughc almost 4 years ago
- 1 comment
#57 - Restructure null model
Pull Request -
State: closed - Opened by amstilp almost 4 years ago
- 7 comments
#56 - K0 values greater than 1
Issue -
State: closed - Opened by sstadick almost 4 years ago
- 1 comment
#55 - What does correctKin do?
Issue -
State: closed - Opened by sstadick almost 4 years ago
- 4 comments
#54 - change small.samp.correct default to TRUE
Pull Request -
State: closed - Opened by smgogarten almost 4 years ago
- 1 comment
#53 - Add error with collinear covariates
Pull Request -
State: closed - Opened by amstilp almost 4 years ago
- 1 comment
#52 - Small null model
Pull Request -
State: closed - Opened by smgogarten almost 4 years ago
- 1 comment
#51 - rename output of jointScoreTest to be consistent with assocTestSingle
Pull Request -
State: closed - Opened by smgogarten almost 4 years ago
- 1 comment
#50 - replace tidyverse with data.table
Pull Request -
State: closed - Opened by smgogarten about 4 years ago
- 2 comments
#49 - add BinomiRare and CMP tests
Pull Request -
State: closed - Opened by smgogarten about 4 years ago
- 3 comments
#48 - Matt branch
Pull Request -
State: closed - Opened by mconomos about 4 years ago
- 1 comment
#47 - parallel implementation of pcrelate
Issue -
State: closed - Opened by dleopold about 4 years ago
- 3 comments
#46 - varCompCI gives a heritability of 0
Issue -
State: closed - Opened by yangli-ai about 4 years ago
- 3 comments
#45 - Effect allele
Pull Request -
State: closed - Opened by smgogarten about 4 years ago
- 2 comments
#44 - Bugfix/single sample blocks
Pull Request -
State: closed - Opened by sstadick about 4 years ago
- 2 comments
#43 - Loss of results when doing a block comparison with a single sample in one of the blocks.
Issue -
State: closed - Opened by sstadick about 4 years ago
- 3 comments
#42 - Add a joint score test function
Pull Request -
State: closed - Opened by amstilp about 4 years ago
- 3 comments
#41 - pcrelate parallel implementation
Issue -
State: closed - Opened by dleopold over 4 years ago
- 2 comments
#40 - fitNullModel fails if AnnotatedDataFrame contains a tibble
Issue -
State: closed - Opened by smgogarten over 4 years ago
- 1 comment
#39 - Force design matrices to be non-sparse
Pull Request -
State: closed - Opened by amstilp over 4 years ago
- 1 comment
#38 - Is it possible to test individual samples against a built model?
Issue -
State: closed - Opened by sstadick over 4 years ago
- 5 comments
#37 - allow divergence to be NULL in pcairPartition
Pull Request -
State: closed - Opened by smgogarten over 4 years ago
- 2 comments
#36 - Fix issue when a starting VC is 0, or small
Pull Request -
State: closed - Opened by mconomos over 4 years ago
- 1 comment
#35 - added check for being a mixed model to varCompCI
Pull Request -
State: closed - Opened by mconomos almost 5 years ago
- 1 comment
#34 - Remove Wald from single variant and burden tests
Pull Request -
State: closed - Opened by mconomos almost 5 years ago
#33 - Saige
Pull Request -
State: closed - Opened by mconomos about 5 years ago
- 1 comment
#32 - Carriers only tests
Pull Request -
State: closed - Opened by jiwonslee about 5 years ago
- 3 comments
#31 - count non missing
Pull Request -
State: closed - Opened by mconomos about 5 years ago
- 1 comment
#30 - bug in assocTestSingle if there are monomorphic SNPs
Issue -
State: closed - Opened by jonaszierer about 5 years ago
- 4 comments
#29 - PCAir unable to proceed when there are no related individuals
Issue -
State: closed - Opened by seunghun23 about 5 years ago
- 3 comments
#28 - error, unable to find an inherited method for function '.readSampleId' for signature
Issue -
State: closed - Opened by jychungbu about 5 years ago
- 9 comments
#27 - update to makeSparseMatrix to work on large matrices
Pull Request -
State: closed - Opened by mconomos about 5 years ago
- 5 comments
#26 - Bug with GxE when using GenotypeIterator
Issue -
State: closed - Opened by jonaszierer about 5 years ago
- 1 comment
#25 - MAC
Pull Request -
State: closed - Opened by smgogarten about 5 years ago
#24 - variable names with "SE" or "Est" crash
Issue -
State: closed - Opened by jonaszierer about 5 years ago
- 1 comment
#23 - add flag of useGWG
Pull Request -
State: closed - Opened by terrytianyuzhang over 5 years ago
#22 - var estimation
Pull Request -
State: closed - Opened by terrytianyuzhang over 5 years ago
#21 - fastSKAT
Pull Request -
State: closed - Opened by smgogarten over 5 years ago
#20 - Nullmod conv
Pull Request -
State: closed - Opened by smgogarten over 5 years ago
#19 - estimating var(T) with GWG
Pull Request -
State: closed - Opened by terrytianyuzhang over 5 years ago
#18 - updated kingToMatrix to account for new KING --related output
Pull Request -
State: closed - Opened by mconomos over 5 years ago
- 1 comment
#17 - remove redundant staff
Pull Request -
State: closed - Opened by terrytianyuzhang over 5 years ago
- 1 comment
#16 - PCG GENESIS first time
Pull Request -
State: closed - Opened by terrytianyuzhang over 5 years ago