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2
votes
1
answer
90
views
1
answer
What is the best and latest package/software for post-processing of Hi-C (Chromosome Conformation Capture)?
gene R next-gen hic gwas written 2 days ago by jamespower • 0 • updated 2 days ago by Alex Reynolds ♦ 23k
3
votes
0
answers
1.4k
views
0
answers
How To Create The .Legend And .Phase Files For Gwas Imputation When Using Mach
gwas imputation plink written 4.7 years ago by mandar.bobade60 • 80 • updated 3 days ago by moushengxu • 300
0
votes
0
answers
39
views
0
answers
How to handle NaN in emmax Kinship matrix?
gwas snp written 4 days ago by CWesse • 0
0
votes
0
answers
71
views
0
answers
How to filter Michigan genotype imputation results
gwas rsq qc imputation written 4 days ago by robjohn70000 • 110
0
votes
0
answers
51
views
0
answers
Claiming two association signals are independent if only summary statistics and reference LD are available
gwas association independent written 7 days ago by Vincent Laufer • 880
5
votes
1
answer
86
views
1
answer
If the odds ratio of a SNP is < 1, does that mean the minor allele is protective?
gwas odds ratio written 7 days ago by maya123z • 10 • updated 7 days ago by Kevin Blighe ♦ 17k
0
votes
0
answers
53
views
0
answers
Random Subset of Individuals from .BED File (.ped not available)
gwas plink written 12 days ago by angus.gane • 0
0
votes
0
answers
82
views
0
answers
PLINK heterozygosity - Negative F statistic?
gwas plink heterozygosity written 16 days ago by Caragh • 40
0
votes
0
answers
83
views
0
answers
Strange Files With EIGENSOFT smartpca
eigensoft gwas pca written 18 days ago by dxm275 • 0 • updated 17 days ago by h.mon ♦ 13k
0
votes
0
answers
65
views
0
answers
What is a good strategy to find hit regions from a GWAS in R?
R genomicranges gwas written 18 days ago by jamespower • 0
2
votes
1
answer
135
views
1
answer
Gene based analysis methods, tools
gene gwas tools methods R written 20 days ago by zx8754 ♦ 4.1k
0
votes
0
answers
109
views
0
answers
GWAS summary file including risk allele, protective allele and disease
protective gwas allele disease risk written 24 days ago by Shicheng Guo • 4.7k
0
votes
0
answers
128
views
0
answers
How to calculate odds ratio in a GWAS using GEMMA output?
gwas odds ratio gemma written 25 days ago by maya123z • 10
3
votes
3
answers
225
views
5 follow
3
answers
Get rsID for a list of SNPs in an entire GWAS sumstats file
sequencing gwas next-gen sumstats written 26 days ago by camerond • 0 • updated 25 days ago by cpad0112 • 4.5k
4
votes
0
answers
129
views
0
answers
Extremely low pve in a GWAS study?
chip heritability gwas pve gemma written 28 days ago by maya123z • 10
3
votes
1
answer
178
views
1
answer
Correcting for population structure in GWAS?
gwas qq plot pca gemma written 4 weeks ago by maya123z • 10 • updated 4 weeks ago by Kevin Blighe ♦ 17k
1
vote
1
answer
128
views
1
answer
How to input covariates in GEMMA?
gwas pca gcta gemma written 4 weeks ago by maya123z • 10
1
vote
1
answer
106
views
1
answer
Converting Affymtrix SNP data to plink and VCF formats
vcf gwas snp plink affymetrix written 4 weeks ago by robjohn70000 • 110 • updated 4 weeks ago by Kevin Blighe ♦ 17k
0
votes
0
answers
94
views
0
answers
Which SNP is the best to use for GWAS from SNP-seek (IRRI) data set?
gwas snp-seek snp genotyping written 5 weeks ago by rizky_dsatrio • 0
2
votes
1
answer
133
views
1
answer
bim and fam downloaded as .txt files, won't work with PLINK?
gwas plink snp written 6 weeks ago by maya123z • 10
23
votes
5
answers
3.2k
views
7 follow
5
answers
Analysis Of Snps In Gene Deserts
annotation snp gwas written 7.5 years ago by Khader Shameer ♦ 17k • updated 6 weeks ago by Biostar ♦♦ 20
1
vote
1
answer
5.4k
views
1
answer
Remove Duplicate Individuals From Plink Ped File Using Plink
gwas plink ped genotype written 4.3 years ago by venkateshr89 • 680 • updated 6 weeks ago by Vale • 0
0
votes
3
answers
644
views
3
answers
Merging files in plink
gwas plink snp written 11 months ago by Tears • 0 • updated 6 weeks ago by Leonida Monaco • 10
0
votes
0
answers
87
views
0
answers
PLINK: TCGA IDs in phenotype file are partial compared to VCF IDs
genome gwas tcga plink software error written 6 weeks ago by emmabirdy • 0
0
votes
0
answers
145
views
0
answers
Differences in the number of genotyping data for GWAS
gwas snp written 7 weeks ago by rizky_dsatrio • 0
0
votes
0
answers
169
views
0
answers
Extra header column stopping EMMAX (C), but not seen in input files
gwas c++ emmax genomics plink written 8 weeks ago by michael.nagle • 90
0
votes
1
answer
2.2k
views
1
answer
How can I analyze the data provided by Michigan Imputation server using ProbABEL?
vcf gwas dosage written 2.3 years ago by sanjana.sundaresan • 0 • updated 7 weeks ago by Teresa • 0
5
votes
2
answers
635
views
2
answers
Software for visualising GWAS results
software gwas code package written 18 months ago by entheologist33 • 70 • updated 8 weeks ago by shuaichengwang • 0
2
votes
0
answers
229
views
0
answers
"Unrecognized token: C" error when using emmax-kin to make kinship matrix for GWAS
gwas kinship emmax genomics written 9 weeks ago by michael.nagle • 90
6
votes
2
answers
179
views
2
answers
Why GWASs cannot speculate what kind of mutation the SNP would cause?
gwas snp written 10 weeks ago by francois • 10 • updated 10 weeks ago by Noushin N • 490
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