genetics-statistics/GEMMA issues and pull requests

#281 - BIMBAM format (preferred)

Issue - State: open - Opened by Sh1ne111 6 months ago

#280 - Identical P-Values at end of run

Issue - State: open - Opened by jeremysutherland 7 months ago

#279 - ERROR: Enforce failed for Problem reading FAM file (phenotypes do not match geno file) in src/gemma_io.cpp at line 600 in ReadFile_fam GEMMA 0.98.3 (2020-11-28) by Xiang Zhou and team (C) 2012-2020

Issue - State: open - Opened by liuye2024 9 months ago

#278 - The problem of filtering snp parameters

Issue - State: open - Opened by hhd1008611 9 months ago

#277 - Why the diagonal of relatedness matrix is not equal to 1 or a constant value?

Issue - State: open - Opened by xiekunwhy over 1 year ago

#276 - WARNING: Brent did not converge

Issue - State: open - Opened by MWQ1224 over 1 year ago

#275 - GSL ERROR: function value is not finite in brent.c at line 58 errno 9

Issue - State: open - Opened by zhoufc213 over 1 year ago

#274 - gsl: newton.c:88: ERROR: function value is not finite 3.08%

Issue - State: open - Opened by jenny315 over 1 year ago

#273 - Got a nan in the p-value results

Issue - State: open - Opened by voichek over 1 year ago - 1 comment

#272 - gemma-wrapper:279:in `<main>': Expected GEMMA -a genotype file switch (RuntimeError)

Issue - State: open - Opened by KizBaolin over 1 year ago

#271 - Pve is .999

Issue - State: open - Opened by aguilar-gomez over 1 year ago

#270 - Categorical covariates

Issue - State: open - Opened by AlexandreHUBERT17 over 1 year ago

#269 - Modified files for strain-specific residual variance option

Pull Request - State: open - Opened by jb621-star over 1 year ago

#268 - Residual Variance additions to mvlmm.cpp

Pull Request - State: closed - Opened by jb621-star over 1 year ago

#267 - The input files includes 26 linkage groups but the output files only includes 22 linkage group

Issue - State: open - Opened by yingxins over 1 year ago

#266 - very low number of analyzed SNPs/var

Issue - State: open - Opened by xbarvazx almost 2 years ago

#265 - Gemma run-time for Estimate Relatedness Matrix calculation

Issue - State: open - Opened by alviitayyaba over 2 years ago

#264 - basic usage doesn't work

Issue - State: closed - Opened by sql647 over 2 years ago

#263 - long haplotype as population structure

Issue - State: open - Opened by amsamani over 2 years ago

#262 - Enforce failed for number of analyzed individuals equals 0. in src/param.cpp at line 2073 in ProcessCvtPhen

Issue - State: open - Opened by zeroLB over 2 years ago - 1 comment

#261 - Parsing input file '' failed in function AnalyzeBimbamGXE

Issue - State: open - Opened by MaxiEstravis over 2 years ago
Labels: Support: use google groups instead

#260 - Issue with GEMMA-Wrapper

Issue - State: open - Opened by vinod1981 almost 3 years ago - 1 comment

#259 - FAILED error

Issue - State: open - Opened by SNgalaxy about 3 years ago - 1 comment
Labels: Track bugs here. Please use google groups instead

#258 - Errors when running GEMMA in an SoS step but ok in command line

Issue - State: open - Opened by zhangbs92 about 3 years ago - 1 comment
Labels: Track bugs here. Please use google groups instead

#257 - Phenotype file format for eQTL analysis

Issue - State: open - Opened by SNgalaxy about 3 years ago
Labels: Track bugs here. Please use google groups instead

#256 - Longitudinal Phenotype data

Issue - State: open - Opened by ryshi06 about 3 years ago - 2 comments
Labels: Track bugs here. Please use google groups instead

#255 - -lmm 9 option leads to bug in mvlmm model

Issue - State: open - Opened by diogro about 3 years ago - 1 comment
Labels: bug, mvlmm

#254 - All snp have missing genotype for all individuals and will be ignored error

Issue - State: open - Opened by kkamii about 3 years ago - 2 comments
Labels: Track bugs here. Please use google groups instead

#253 - The gemma model choose problem

Issue - State: closed - Opened by K-zhangfengwei over 3 years ago - 1 comment

#252 - GEMMA ERROR

Issue - State: open - Opened by sekhwal over 3 years ago
Labels: Track bugs here. Please use google groups instead

#251 - How to find Significant SNPs from the results of GEMMA

Issue - State: open - Opened by sekhwal over 3 years ago
Labels: Track bugs here. Please use google groups instead

#250 - compute fix effect

Issue - State: open - Opened by xixifa over 3 years ago
Labels: Track bugs here. Please use google groups instead

#249 - GSL ERROR: matrix is singular in lu.c at line 147 errno 1

Issue - State: open - Opened by AgatheMaupetit over 3 years ago
Labels: Track bugs here. Please use google groups instead

#248 - Should I use the "beta" estimates as the allelic effect size?

Issue - State: open - Opened by DuttaAnik over 3 years ago
Labels: Track bugs here. Please use google groups instead

#247 - Test failures for 0.98.4 on CentOS 7

Issue - State: closed - Opened by verdurin over 3 years ago - 1 comment
Labels: bug, add tests

#246 - Suggestion: link to R's gemma2?

Issue - State: closed - Opened by richelbilderbeek over 3 years ago - 5 comments
Labels: enhancement, documentation, Please help, See gemma2/lib

#245 - GEMMA output error

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

#244 - Beta for meta-analysis from MVLMM GEMMA output

Issue - State: open - Opened by som-soremekun over 3 years ago
Labels: Track bugs here. Please use google groups instead

#243 - Multivariate GEMMA hangs forever

Issue - State: open - Opened by biona001 over 3 years ago - 6 comments
Labels: bug

#242 - Debian bug fails unit test

Issue - State: closed - Opened by pjotrp over 3 years ago - 2 comments
Labels: add tests

#241 - LMM GXE bimbam read problem

Issue - State: open - Opened by tplinderoth over 3 years ago
Labels: bug

#240 - Major allelle influences additive effect sign

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

#239 - Error in `gemma': free(): invalid pointer: 0x00007fd0e37cbe7a

Issue - State: closed - Opened by clsgithubusr over 3 years ago - 2 comments
Labels: bug

#238 - Correct for X chromosome

Issue - State: open - Opened by pjotrp almost 4 years ago
Labels: bug

#237 - LMM output missing something?

Issue - State: closed - Opened by pjotrp almost 4 years ago - 5 comments
Labels: bug, lmm

#236 - Difficulties in understanding mvLMM output

Issue - State: closed - Opened by shafiqnoa almost 4 years ago - 1 comment
Labels: Support: use google groups instead

#235 - Additive effect

Issue - State: open - Opened by pjotrp almost 4 years ago
Labels: enhancement, high priority, documentation

#234 - Allow and describe options for disabling filters

Issue - State: open - Opened by pjotrp about 4 years ago - 6 comments
Labels: enhancement, See gemma2/lib

#233 - Fix Travis CI

Issue - State: closed - Opened by pjotrp about 4 years ago - 2 comments
Labels: add tests

#232 - Possibel way to output the random effects?

Issue - State: closed - Opened by TeaByrd about 4 years ago
Labels: Support: use google groups instead, Track bugs here. Please use google groups instead

#231 - Issue with all SNPs being filtered out

Issue - State: closed - Opened by jenncoughlan about 4 years ago
Labels: Support: use google groups instead, Track bugs here. Please use google groups instead, See gemma2/lib

#230 - -lopenblas library not found

Issue - State: closed - Opened by Marisa89 about 4 years ago - 4 comments
Labels: enhancement, Support: use google groups instead, timed out

#229 - GSL ERROR: matrix is singular in lu.c at line 262 errno 1 mvLMM 19 phenotypes

Issue - State: closed - Opened by TeaByrd about 4 years ago - 1 comment

#228 - GSL ERROR: matrix is singular in lu.c at line 262 errno 1

Issue - State: closed - Opened by pwang16 over 4 years ago - 3 comments

#227 - GSL ERROR

Issue - State: closed - Opened by voichek over 4 years ago - 2 comments

#226 - mvLMM results in exactly zero (0.000000e+00) p-values

Issue - State: closed - Opened by dgarrimar over 4 years ago - 1 comment

#225 - Including -gxe produces error: GSL ERROR: function value is not finite in brent.c at line 58 errno 9

Issue - State: closed - Opened by DeWitP over 4 years ago - 2 comments

#224 - after 72 hours running, there was no output results

Issue - State: closed - Opened by xiaoxihe over 4 years ago - 3 comments
Labels: timed out

#223 - Generating Kinship Matrix

Issue - State: closed - Opened by baigal628 over 4 years ago - 2 comments

#222 - GSL ERROR: function value is not finite in newton.c at line 88 errno 9

Issue - State: closed - Opened by baigal628 over 4 years ago - 3 comments
Labels: Track bugs here. Please use google groups instead

#221 - two questions on mvLMM

Issue - State: closed - Opened by arkyl over 4 years ago - 4 comments
Labels: Track bugs here. Please use google groups instead

#220 - ERROR: Enforce failed for Problem reading FAM file (phenotypes out of range) in src/gemma_io.cpp at line 600 in ReadFile_fam

Issue - State: closed - Opened by Jarod-R over 4 years ago - 5 comments

#219 - ERROR: Enforce failed for file_kin .cXX.txt

Issue - State: closed - Opened by jdleal over 4 years ago
Labels: Track bugs here. Please use google groups instead

#218 - Gemma Conda version is really slow

Issue - State: closed - Opened by yujun2017 over 4 years ago - 1 comment

#216 - Build time test suite error in Debian package

Issue - State: closed - Opened by tillea over 4 years ago - 7 comments
Labels: bug, high priority

#215 - ERROR：number of total SNPs/var do not equal to number of analyzed SNPs

Issue - State: closed - Opened by wangxuann1995 over 4 years ago - 2 comments
Labels: Support: use google groups instead, Track bugs here. Please use google groups instead

#214 - ERROR: Enforce failed for number of analyzed individuals equals 0. in src/param.cpp at line 2061 in ProcessCvtPhen

Issue - State: closed - Opened by alioniya over 4 years ago - 2 comments
Labels: Track bugs here. Please use google groups instead

GitHub / genetics-statistics/GEMMA issues and pull requests