User: chloe.p.oconnell

Reputation:
80
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New User
Location:
United States
Last seen:
3 years ago
Joined:
4 years, 5 months ago
Email:
c***************@gmail.com

Posts by chloe.p.oconnell

<prev • 9 results • page 1 of 1 • next >
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Imputing SNP information - SNP chip
... Hi,  I have genotype information for ~680 SNPs in each of my subjects across the genome. For each subject, there are one or two SNPs that are not genotyped. Given that I don't have any read information or any additional information on the genotypes of these SNPs in these subjects, what is the best ...
snp written 3.1 years ago by chloe.p.oconnell80 • updated 3.0 years ago by Biostar ♦♦ 20
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Comment: C: GSEA with ranked list
... Thanks for the help. For some reason, it isn't working correctly. I'm assuming this is my issue, as my coding background is rather weak. I'll keep trying... ...
written 4.4 years ago by chloe.p.oconnell80
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GSEA with ranked list
... Hi,    I'm trying to run GSEA on a ranked list of genes. In other words, I'm not using expression data (instead, I'm using a list of genes ranked by the prevalence of variants in those genes in my dataset). I can't figure out how to run GSEA using non-standard input files - either the desktop vers ...
variant calling tutorials gsea snp written 4.4 years ago by chloe.p.oconnell80
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Comment: C: Gene length database
... Is it possible to do this in python? ...
written 4.4 years ago by chloe.p.oconnell80
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Gene length database
... Hi,  I'm trying to do a pathways/enrichment analysis and in order to do so, I'm trying to divide the prevalence of a variant in a gene by the length of the gene. Is there a database online where I can easily download gene lengths? I'm working with gene symbols (i.e. KCNQ2) so anything that matched ...
ncbi database gene length written 4.4 years ago by chloe.p.oconnell80 • updated 2.6 years ago by anp375140
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Comment: A: Weighted Pathways Analysis
... I was under the impression that GSEA only does expression enrichment stuff and common variant stuff, and wasn't applicable to rare variant analysis. Correct me if I'm wrong.  ...
written 4.4 years ago by chloe.p.oconnell80
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Comment: A: Weighted Pathways Analysis
... It is a list of rare, high-impact variants. I converted the list of variants to a list of genes, and want to account for the fact that in my sample there are some genes that house a variant in 40% of my subjects and other genes that only house a variant in 2%. ...
written 4.4 years ago by chloe.p.oconnell80
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Weighted Pathways Analysis
... I'm trying to do a pathways analysis/check for gene set enrichment on a list of genes. Right now I'm using DAVID, but that doesn't allow me to rank/weight my genes (i.e. give higher priority to genes that appear more often in my list). Does anyone know of a tool that allows you to do pathways analys ...
pathways analysis variant gsea written 4.4 years ago by chloe.p.oconnell80 • updated 4.4 years ago by Biostar ♦♦ 20
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Variant prevalence not listed
... Hi,  I'm completing a variant analysis of rare variants found in the genomes of my cases vs. controls. I'm only looking at rare variants (variants where the alternate allele is present in less than 1% of the population, as determined by the 1000 genomes project alternate allele frequency). However, ...
rs 1000 genomes project variant snp sequencing written 4.5 years ago by chloe.p.oconnell80 • updated 4.4 years ago by rbagnall1.3k

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Popular Question 4.4 years ago, created a question with more than 1,000 views. For GSEA with ranked list

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