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• Estimating the effective number of tests from an AR1 model
  Hi All, I'm performing admixture analysis using the [BMIX method][1] and I need to estimate the...
• how to estimate founder and effective population size from snps data in VCF format
  Hi everyone, I have a filtered SNPS sequence data in VCF format. I need to use this data to esti...
• How to calculate the effective population size of part of a recently admixed genome?
  I have a SNP panel (1 million SNPs) of an African American cohort. Is there any way to calculate ...
• Effects of cohort size on survival estimation
  Hello, I'm currently working on survival analyses using different cohorts. I found a striking ev...
• Linear mixed model for genome-wide association analysis
  Dear all, I would like to apply the linear mixed model on a cohort study to assess the effect of...
• Area under the ROC Curve for genetic data
  Hi Biostar. I have performed logistic regression on 3 independent sets of case/control cohorts. ...
• selecting short regions with multiple SNPs to write to a fasta file using SNP data generated from short read data
  Hi, I am trying to do an analysis that requires sequence data, and not SNPs directly (Extended B...
• Getting A Table Of Genotypes (Snps) Into A Genome Browser
  I work with a non-model organism which is absent from online genome browsers. I have genotypes at...
• What is the best statistics to rank a gene list for GSEA analysis?
  Hi, I have expression values for around 20,000 genes in 100 different individuals. I need to ran...
• SNP IDs changed when making .ped files using PLINK
  I have data on genetic variants for multiple individuals for a family in the form of a .vcf file....
• Compare SNP frequency of patient cohort to DBSNP and test for significance
  Hi, I have analyzed the sequencing data of a patient cohort and found some SNPs that occur in a ...
• Is it possible to extract the C component of the ACE model from an AE model?
  Dear all, I calculated the estimates of the variance explained of a set of quantitative phenotyp...
• Deviation from HWE by Comparing One Genes SNPs to Rest of the Cohort
  Hi all, I am trying to compare the SNPs from a "target gene" to the SNPs of genes from the rest ...
• Assigning locus to set of SNPs based on its chromosome position
  Hi all,     So I have this tab-delim file with information on (following columns) SNP    CHR ...
• Qc Of A New Study Sample In A Cost-Effective Way
  Hi everyone, Very soon we will have DNA on a very large cohort (more than 30K IDs). We would lik...
• Principal component analysis
  Hello, I have done a principal component analysis based on 250 SNPs from a single locus of 100 d...
• Where to download official reference and alternative alleles from 1000 Genomes?
  Hello, using Plink 1.9, I merged to cohorts of individuals that were genotyped at the same ~17000...
• Estimating effective population size (Ne) using ~1 million SNPs
  Is there a tool/software package that can compute Effective Population Size (Ne) based on LD in ~...
• SNps and calculation of sample size
  hi, this is a new area far from my expertise and I want to check if a specific gene has SNPs but...