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Resources for finding out the allele frequency of a SNV by subpopulation
SNP Allele Frequency MAF subpopulation
7.0 years ago by LauferVA 4.2k
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2
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1.9k
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Is it necessary to have all 3 genotypes to report a significant expression quantitative trait locus?
eQTL
updated 7.0 years ago by 20 • written 7.2 years ago by 4.2k
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1
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1.7k
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Calculating LD between specific alleles even if they are not the minor alleles
linkage disequilibrium matrix calculation
7.1 years ago by LauferVA 4.2k
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0
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1.2k
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Estimating epigenetic missing heredity
missing hertability epigenetics
7.1 years ago by LauferVA 4.2k
4
votes
3
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2.1k
views
Adding gene diagram to output from snp.plotter
LD heatmap gene diagram
updated 7.3 years ago by ▴ 350 • written 7.3 years ago by 4.2k
1
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2.8k
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Locus Zoom issues no error but prints file with no LD information displayed
LocusZoom LD Linkage Disequilibrium
7.3 years ago by LauferVA 4.2k
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2.9k
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Locus Zoom issuing an error in valid.viewport()
locus zoom
7.4 years ago by LauferVA 4.2k
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0
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1.3k
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Are there cases in which the association from a GWAS study has been shown to be caused by a SV or CNV?
GWAS CNV causal missing heritablity
7.6 years ago by LauferVA 4.2k
1
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1
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4.8k
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Plink - resolving heterozygous haploid genotypes if an XY chromosome is already assigned in GWAS
Plink GWAS
updated 7.7 years ago by ▴ 10 • written 7.7 years ago by 4.2k
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3
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1.5k
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Return the Title and URL of ~100 pubmed queries to a flat file
pubmed batch query
7.7 years ago by LauferVA 4.2k
0
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1
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1.3k
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Input into GO in such a way as to not receive ambiguous identifier warnings
GO gene symbol HGNC
updated 7.7 years ago by 7.5k • written 7.7 years ago by 4.2k
11
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3
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5.3k
views
Is it valid to call this an "empirical p-value" ?
simulation testing p-value permutation testing
updated 7.8 years ago by 104k • written 7.8 years ago by 4.2k
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1
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2.7k
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Making a standardized list of conversion of all kgp identifiers to RSids for the NHGRI GWAS catalog
kgp rsid conversion SNP
7.8 years ago by LauferVA 4.2k
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1.2k
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Help finding citation that SNPs whose allele frequency has changed much between ethnicities are more likely to be GWAS index SNPs?
GWAS association index SNP
7.8 years ago by LauferVA 4.2k
6
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3
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1.9k
views
Running 1.5M potentially different generalized linear models depending on distribution of read depth information to study CNV
CNV GLM read depth
updated 7.9 years ago by 12k • written 7.9 years ago by 4.2k
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1
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1.9k
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Generalization of the concept of LD to polyallelic variants and / or variants that are within SV and CNV events
linkage disequilibrium LD CNV SV SNV
8.0 years ago by LauferVA 4.2k
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1.7k
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What software was used to produce Figure 1 of this manuscript
Figures linkage disequilbrium GWAS
8.1 years ago by LauferVA 4.2k
7
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6
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4.0k
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how can I get MAF stratified by subpopulation for ASW, or CEU and YRI
genetics MAF subpopulation allele-frequency
updated 2.1 years ago by 43k • written 9.3 years ago by 4.2k
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0
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1.6k
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How to prioritize candidate causal variation and isolate independent association signals in a family based study of catfish
GWAS Causal Variant Association QFAM Family
8.1 years ago by LauferVA 4.2k
3
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2
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1.9k
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Detecting fine population structure such as might confound a rare variant association study
confound rare-variant population GWAS substructure
updated 19 months ago by 43k • written 8.7 years ago by 4.2k
5
votes
5
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2.9k
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Obtain sequences to test positive selection using dN/dS statistics?
positive-selection evolution dN-dS
updated 21 months ago by 43k • written 8.2 years ago by 4.2k
3
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1
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3.3k
views
PAMLX yn00 does not issue error message but prints empty files when asked for dN/dS statistics
dNdS PAML
updated 21 months ago by 43k • written 8.3 years ago by 4.2k
4
votes
1
reply
2.2k
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Formulating the best imputation strategy for multiple GWAS chips in an admixed population
GWAS imputation admixture meta analysis
8.5 years ago by LauferVA 4.2k
6
votes
8
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3.0k
views
List of causal variants for autoimmune diseases
autoimmune SNP GWAS genetics
updated 17 months ago by 43k • written 9.1 years ago by 4.2k
0
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2
replies
2.0k
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Finding public ChIP-seq data for various tissue types
ChIP-Seq
updated 13 months ago by 43k • written 8.6 years ago by 4.2k
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2
replies
3.3k
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Odds Ratio Confidence Intervals in SNP Test
Confidence-Interval OR CI SNPtest
updated 18 months ago by 43k • written 8.8 years ago by 4.2k
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0
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1.9k
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How to find appropriate control regions for gene burden tests on T-cell enhancer regions
gene-burden enhancer control
8.8 years ago by LauferVA 4.2k
0
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0
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1.6k
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Theoretical problems using PCA to control for cases and controls with different ethnicity
GWAS PCA
updated 16 months ago by 43k • written 8.9 years ago by 4.2k
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0
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1.8k
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Most common method for looking at LD independent SNPs
Immunochip GWAS Bonferonni IChip LD
updated 16 months ago by 43k • written 8.9 years ago by 4.2k
0
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2
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1.8k
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Genes with "AK#### or BC#####" in UCSC genome browser
UCSC gene track
updated 22 months ago by 43k • written 9.0 years ago by 4.2k
4
votes
2
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3.8k
views
Using EPACTS to implement SKAT-O - question about ped files
SKAT EPACTS PED
updated 2.1 years ago by 43k • written 9.4 years ago by 4.2k
0
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0
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2.1k
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Which HapMap Citation to cite if pulling information from dbSNP
MAF hapmap dbsnp
updated 23 months ago by 43k • written 9.1 years ago by 4.2k
6
votes
1
reply
5.3k
views
Rationale for including a certain number of PCs in a GWAS study?
PCA Statistics GWAS
updated 9.3 years ago by ★ 4.7k • written 9.3 years ago by 4.2k
0
votes
1
reply
2.1k
views
Getting colors when displaying .bed files in locuszoom1.3
bed locuszoom graph
updated 2.1 years ago by 43k • written 9.3 years ago by 4.2k
2
votes
2
replies
2.9k
views
Bonferonni Correction for mostly overlapping enhancers
statistics bonferonni enhancers
updated 2.1 years ago by 43k • written 9.4 years ago by 4.2k
6
votes
2
replies
2.5k
views
Options for generation of publication quality gene diagrams with annotation
VCF NGS Gene-Annotation
updated 2.3 years ago by 43k • written 9.6 years ago by 4.2k
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