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saigegit
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SAIGE
Development for SAIGE and SAIGE-GENE(+)
GNU General Public License v3.0
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Dominant and Recessive models
#99
surakshavinod
opened
1 year ago
0
Minor allele count in SAIGE vs SAIGE-GENE
#98
daniel-hui
closed
1 year ago
1
Error while installing saige in slurm module
#97
akhilpampana
closed
1 year ago
1
floating point exception raised during step2 SPAtests
#96
mstapylton
opened
1 year ago
1
SAIGE License Clarification
#95
pettyalex
opened
1 year ago
0
Saige gwas giving SE == 0
#94
akhilpampana
opened
1 year ago
3
Saige Docker in google cloud registry
#93
akhilpampana
closed
1 year ago
6
Can you please create tags for released versions?
#92
pettyalex
opened
1 year ago
2
ERROR: 2 has Phased = 2 (not 0)
#91
raminsalmas
closed
1 year ago
1
Update ComputeExact to use vectors rather than raw memory where easy
#90
pettyalex
closed
1 year ago
1
fix: crash in efficient resampling
#89
pettyalex
closed
1 year ago
1
Crash in step 2 with: mean(): object has no elements
#88
pettyalex
closed
1 year ago
13
full grm designation in fitNULLGLMM
#87
jyjo43043
opened
1 year ago
1
Overlap of samples in inputGenoFile and Model File for Step2 GBAT
#86
Ankeet3
closed
1 year ago
1
Markers in 'RegionFile' are not in 'GenoFile'. The chunk is empty (Set Based Tests; Step 2)
#85
surakshavinod
opened
1 year ago
1
INFO scores
#84
MatthewMaher
opened
1 year ago
0
Step 2 segfault and core dump
#83
DDochtermann
opened
1 year ago
2
WARNING: variance of the phenotype is much smaller than 1. Please consider invNormalize=T [SAIGE-GENE]
#82
surakshavinod
opened
1 year ago
2
Error in paste("This is a", AnalysisType, "level analysis.") : object 'AnalysisType' not found Calls: SPAGMMATtest -> SAIGE.Region -> paste
#81
daniel-hui
opened
1 year ago
2
How to create groupfile?
#80
Ankeet3
opened
1 year ago
2
No parameter for "IsDropMissingDosages", how to handle values not present in VCF?
#79
Ankeet3
closed
1 year ago
1
Inverse normal transformation for quantitative traits
#78
cjfei18
opened
1 year ago
0
Back calculated SE
#77
tom-a-bond
closed
1 year ago
2
step2_SPAtests.R: error: Error in getopt(spec = spec, opt = args) : long flag "numLinesOutput" is invalid
#76
surakshavinod
opened
1 year ago
1
DNANexus - Step 2 Error: Error in SPAGMMATtest
#75
ncc95
opened
1 year ago
0
SAIGE installation error
#74
kousikbioinfo
closed
1 year ago
1
Step 1 Killed by R to Protect from Stack Overflow
#73
guarelin
closed
1 year ago
3
Getting the right groupfiles to use for step 2 SAIGE GWAS Gene and Region Based Association Tests
#72
Ankeet3
opened
1 year ago
4
Error in getopt(spec = spec, opt = args) : long flag "start" is invalid
#71
gauri-nagavkar
opened
1 year ago
2
"No markers are left!" error in logs for SAIGE GWAS - gene and region based associations results
#70
Ankeet3
closed
1 year ago
1
double free or corruption & memory not mapped
#69
changxuling
closed
1 year ago
3
Download failed with error 503 for: //github.com/statgen/savvy/archive/v2.1.0.tar.gz
#68
7JVST
closed
1 year ago
1
Step 2 - get_newPhi_scaleFactor error in SAIGE-GENE+
#67
cjfei18
opened
1 year ago
0
Calculating odds ratios from saige-gene summary stats
#66
oalavijeh
closed
1 year ago
1
Imputation of missing genotypes
#65
daniel-hui
closed
1 year ago
1
--isCovariateOffset option and functionality
#64
kousathanas
closed
1 year ago
1
SKATO BURDEN and SKAT p value
#63
wenluo711
opened
1 year ago
6
Standardize default arguments between R and command line and fix MAC thresholds
#62
dvg-p4
opened
1 year ago
1
Default for `--maxMAF_in_groupTest` is not what the help message says it is
#61
dvg-p4
closed
1 year ago
1
NA/1.0/0.0 results for SAIGE-GENE+ when MAC = 10
#60
dvg-p4
closed
1 year ago
3
Is there a dokcer image available yet for 1.1.6.2
#59
qiyubio
closed
1 year ago
1
Attempt to fix Step 2 crash if a region is empty
#58
dvg-p4
closed
1 year ago
0
Longer step 1 runtimes when compared to SAIGE 0.44.2
#57
dvg-p4
closed
1 year ago
1
SAIGE-Gene+ Step 2 crashes if a region is empty
#56
dvg-p4
closed
1 year ago
3
Can --invNormalize be turned off for any value of variance?
#55
mariosaare
closed
1 year ago
1
Installation error "Failed to build package statgen/savvy"
#54
daniel-hui
closed
1 year ago
4
Documentation site for saige-gene+ step 2 seem broken
#53
Alexander-Stuckey
closed
1 year ago
1
Optimum plink file for Null and use of Sparse GRM
#52
Richard-Packer
closed
1 year ago
1
Justification for 0.125 GRM sparsity threshold
#51
tom-a-bond
closed
1 year ago
2
About Pvalue
#50
SheaCheng2000
closed
1 year ago
4
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