Question: User Friendly Tools For Genetic Association Studies (update)
3
gravatar for Thomas
4.9 years ago by
Thomas720
Copenhagen, DK
Thomas720 wrote:

Hi all,


I am giving a course presenting various bioinformatic tools applied in genetic association studies. The target audience are phd students with a medical/biological background. Since non of the students have experience within programming/linux/R etc I will like to focus on "user friendly (web-based)" tools like the following:

SNAP - investigate LD, find out whether a SNP is on GWAS arrays
Hapmap, haploview - select tag SNPs
locusZOOM - visualize association plots
UCSC - investigate the properties/positions etc of SNPs
plink - make association studies and QC for GWAS data
NHLBI Exome Sequencing Project (ESP) - Get sequence derived SNP information
regulomeDB - Get putative functional annotation for SNPs  
HaploReg - Combine LD (1000G) and regulomeDB


I actually asked the same question 2 years back (User Friendly Tools For Genetic Association Studies)  and received some very nice inputs. However, since I am giving the same course again :) I would like to hear if anyone would help renew/expand the existing list.

Thanks a lot,
Thomas

 

ADD COMMENTlink written 4.9 years ago by Thomas720
1

Mostly designed for simple traits, but it is quick and works from VCF files.

 

https://github.com/jewmanchue/vcflib/wiki

ADD REPLYlink modified 4.9 years ago • written 4.9 years ago by Zev.Kronenberg11k
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