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Why may BOLT-LMM and SAIGE (quantitative, linear-mixed model) yield different results when ran on the absolutely the same dataset?
gwas saige replication of results bolt-lmm written 14 hours ago by futurolog • 10 • updated 3 hours ago by GenoMax ♦ 94k
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Why does GWAS Catalog mix OR and beta in the same column?
gwas_catalog gwas or written 6 months ago by Juan Manuel Berros • 90 • updated 1 day ago by zhoufeng2ye • 0
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How to get independent loci from gwas variants
gwas python R snp sequencing written 2 days ago by morse.endeavour86 • 0
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Math behind association with PLINK
gwas association plink written 2 days ago by Will • 0 • updated 2 days ago by rpolicastro ♦ 3.1k
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Convert ped/bed into CSV/text file
gwas machine learning plink written 10 weeks ago by Dhara Awasthi • 20 • updated 3 days ago by Biostar ♦♦ 20
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Deviance in allele frequencies between arrays and WGS
array gwas prs wgs written 11 days ago by German.M.Demidov • 1.9k
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Plotting the results (p-values) from various conditional GWAS
gwas plot written 11 days ago by sam.far.7 • 0 • updated 11 days ago by devarora • 240
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Plink And Missing Values
p-value gwas plink written 7.0 years ago by RawRaw • 0 • updated 16 days ago by Biostar ♦♦ 20
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Understanding LD with tassel results
gwas linkage disequilibrium tassel ld gbs written 2.1 years ago by alesierra28 • 0 • updated 17 days ago by kamalthind003 • 0
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Categorize genotype data into 0s,1s and 2s to run GWAS
gwas non-additive genotype written 23 days ago by doodle • 30 • updated 19 days ago by Kevin Blighe ♦ 69k
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Nonlinear longitudinal GWAS analysis software -- anything user friendly out there?
software gwas longitudinal nonlinear written 4 weeks ago by david.siegel • 0
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GWAS on a twin sample
gwas relatedness twin gcta gemma written 10 months ago by javadjamshidi • 40 • updated 27 days ago by Biostar ♦♦ 20
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How to open HUGE excel files with genomic info
R sequencing snp gwas written 29 days ago by simone.castellana • 10 • updated 29 days ago by Mensur Dlakic • 8.1k
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bim and fam downloaded as .txt files, won't work with PLINK?
gwas plink snp written 2.8 years ago by maya123z • 40 • updated 4 weeks ago by Biostar ♦♦ 20
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Error when importing dosage file using PLINK2 for imputation analysis
gwas plink2 imputation plink dosage_file written 4 weeks ago by hkj7 • 0 • updated 4 weeks ago by _r_am ♦ 32k
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The same effect of SNPs in LD?
gwas linkage disequilibrium effect size written 5 weeks ago by seta • 1.4k
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How to include BETA and SE in output of METAL
gwas beta metagwas metal se written 5 weeks ago by anamaria • 140 • updated 5 weeks ago by _r_am ♦ 32k
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Is there a reason to limit dummy coding these alleles as 0 or 1 in this regression model example, instead of allowing values of 0,1,or 2?
gwas logistic regression written 6 weeks ago by curious • 470
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Linking SNPs to their summary statistics - if any -
gwas snps statistics written 6 weeks ago by SGMS • 70
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113
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Adding SNP/Gene labels to a qqplot using qqman
gwas qqman qqplot R written 7 weeks ago by tacrolimus • 80
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Error Reading PLINK files (.bed)
gwas .bed plink read.plink written 3.4 years ago by eduardorazza • 0 • updated 7 weeks ago by Biostar ♦♦ 20
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compare two GWAS results
gwas snp written 7 weeks ago by sihambarkus • 0 • updated 7 weeks ago by Shicheng Guo • 8.5k
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124
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CNV data from Illumina OncoArray Cheap analysis
snpchip cnv gwas written 7 weeks ago by melania 2282 • 100
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Question about Risk Scores
R prs snp risk scores gwas written 7 weeks ago by lisaks • 20 • updated 7 weeks ago by Kevin Blighe ♦ 69k
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What is the smallest number of cases you can have in a GWAS before interpretation starts becoming troublesome
gwas written 8 weeks ago by curious • 470
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How to check mitochondrial reference in GWAS data for HaploGrep analysis
mtdna gwas haplogroup snp haplogrep2 written 3 months ago by irieljoerin • 40 • updated 8 weeks ago by Jeremy Leipzig ♦ 19k
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locuszoom on a HPC - LD could not be computed for SNP
hpc locuszoom gwas bash written 8 weeks ago by tacrolimus • 80
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164
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PLINK beta coefficient
gwas association plink beta coefficient written 8 weeks ago by seta • 1.4k
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Individual-level data for Million Veteran Program (MVP)
mvp gwas written 8 weeks ago by Shicheng Guo • 8.5k • updated 8 weeks ago by kvshamsudheen • 60
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Convert CSV to PED
gwas plink written 10 weeks ago by Dhara Awasthi • 20
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