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Gene Set Enrichment Analysis using Variant Density instead of Expression levels?
R GSEA Density Enrichment
updated 4.4 years ago by 20 • written 7.9 years ago by ▴ 180
2
votes
0
replies
1.5k
views
Statistical Genetics - What information is required for haplotype phasing in a novel, admixed population?
admixture phasing haplotype exome
6.0 years ago by anp375 ▴ 180
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1.5k
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Tool for Pathway Analysis on SKAT results
SKAT DNA-Seq Exome Pathway Analysis
6.4 years ago by anp375 ▴ 180
1
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2
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2.2k
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How can I remove Indels from a VCF file that are actually microsatellite variants?
microsatellite indel
updated 6.5 years ago by 161k • written 6.5 years ago by ▴ 180
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2
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7.2k
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What are the typical IBD PIHAT values calculated by PLINK for duplicate samples?
plink IBD
updated 6.5 years ago by ★ 2.1k • written 6.5 years ago by ▴ 180
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0
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1.3k
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Is there a phasing algorithm or tool that first determines undeniably present haplotypes?
phasing hardy weinberg haplotype beagle
6.8 years ago by anp375 ▴ 180
2
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4
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1.4k
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How do you interpret the presence of only one homozygote in a population, with no heterozygotes?
zygosity biology somatic germline
7.1 years ago by anp375 ▴ 180
3
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2
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1.4k
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Would a complete lack of heterozygotes in a population indicate the presence of a recessive allele?
genetics zygosity
updated 7.3 years ago by 20k • written 7.3 years ago by ▴ 180
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1
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3.5k
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Using VEP: Variant Effect Predictor, how do I get the 1000G global Allele Frequency of my alternate alleles specifically?
VEP Variant Effect Predictor Annovar
updated 7.4 years ago by ▴ 570 • written 7.6 years ago by ▴ 180
2
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3
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2.5k
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How do I get GO term annotations using VEP?
ensembl GO VEP gene ontology
updated 2.6 years ago by ★ 2.4k • written 7.5 years ago by ▴ 180
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0
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1.9k
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How do I get Genbank files by using wiki gene ids in bioperl?
bioperl genbank
updated 15 months ago by 43k • written 9.0 years ago by ▴ 180
0
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0
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2.4k
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Are GERP RS scores for a variant specific for the alternate allele or just the region?
GERP RS Annovar
7.6 years ago by anp375 ▴ 180
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0
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1.2k
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For anyone who has used SKAT for association with genes as sets
skat association SNP
7.6 years ago by anp375 ▴ 180
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0
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1.7k
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What causes missing GERP scores in Annovar results?
Annovar GERP
7.7 years ago by anp375 ▴ 180
2
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0
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4.5k
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How should I calculate the variant density, per kb for a gene, for two different groups in a case/control study?
density case/control
7.8 years ago by anp375 ▴ 180
2
votes
5
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2.6k
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Ingenuity Pathway Analysis by Variant Density?
IPA Pathway Density Variant
7.8 years ago by anp375 ▴ 180
3
votes
2
replies
2.1k
views
How do I get the lengths of different regions targeted by the Nextera expanded rapid capture exome kit for b37?
exome nextera lengths
updated 8.0 years ago by ★ 2.1k • written 8.0 years ago by ▴ 180
1
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5
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2.0k
views
What's the maximum number of threads that bwa mem can handle?
bwa mem threads
updated 8.1 years ago by 7.3k • written 8.1 years ago by ▴ 180
1
vote
1
reply
1.2k
views
Is a vcf file necessary in IndelRealigner if we already used it to make intervals?
IndelRealigner RealignerTargetCreator vcf GATK
updated 8.1 years ago by ★ 2.1k • written 8.1 years ago by ▴ 180
4
votes
3
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4.2k
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Problem using PicardTools MarkDuplicates: Value Was Put Into Pairinfomap More Than Once
PicardTools Picard MarkDuplicates Pairinfomap
updated 8.1 years ago by 10k • written 8.1 years ago by ▴ 180
0
votes
1
reply
1.9k
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Perl module to handle the CCDS file
CCDS Perl
updated 17 months ago by 43k • written 8.8 years ago by ▴ 180
0
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0
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1.6k
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Is there a Perl script to use Biomart ID conversion?
biomart bioperl perl id conversion
updated 8.8 years ago by 20 • written 9.0 years ago by ▴ 180
4
votes
5
replies
18k
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Genbank identifiers vs Entrez Gene ID?
bioperl ccds genbank entrezgene
updated 16 months ago by 43k • written 8.9 years ago by ▴ 180
0
votes
4
replies
2.6k
views
GO descriptions not printing out
GOTerm bioperl
updated 15 months ago by 43k • written 9.0 years ago by ▴ 180
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