I am very glad to see that you guys are building an ecosystem for VCF formatted GWAS files.
There are 4 new tools, all published this year. I tested and found them very easy to implement and quite important for functional analyses. It would be great if you guys could consider adding them.
For genetic architecture, iCPAGdb, published at Genome Medicine: "An atlas connecting shared genetic architecture of human diseases and molecular phenotypes provides insight into COVID-19 susceptibility".
For colocalization, hyprcoloc, published at Nature Communications: "A fast and efficient colocalization algorithm for identifying shared genetic risk factors across multiple traits".
For drug target analysis (maybe add as a new category), Trans-Phar, published at Human Molecular Biology: “Integration of genetically regulated gene expression and pharmacological library provides therapeutic drug candidates".
For enrichment analysis (maybe add as a new category "enrichment"), clusterProfiler, published at The Innovation: "clusterProfiler 4.0: A universal enrichment tool for interpreting omics data".
Finally, I feel it is very important to add a new category for (cross-traits) meta-analysis. A lot of reserachers would want to do this when a lot of GWAS are available. This includes the traditional MTAG software, a new PLEIO software published this year at AJHG: "a method to map and interpret pleiotropic loci with GWAS summary statistics"
Hi, there:
I am very glad to see that you guys are building an ecosystem for VCF formatted GWAS files.
There are 4 new tools, all published this year. I tested and found them very easy to implement and quite important for functional analyses. It would be great if you guys could consider adding them.
For genetic architecture, iCPAGdb, published at Genome Medicine: "An atlas connecting shared genetic architecture of human diseases and molecular phenotypes provides insight into COVID-19 susceptibility".
For colocalization, hyprcoloc, published at Nature Communications: "A fast and efficient colocalization algorithm for identifying shared genetic risk factors across multiple traits".
For drug target analysis (maybe add as a new category), Trans-Phar, published at Human Molecular Biology: “Integration of genetically regulated gene expression and pharmacological library provides therapeutic drug candidates".
For enrichment analysis (maybe add as a new category "enrichment"), clusterProfiler, published at The Innovation: "clusterProfiler 4.0: A universal enrichment tool for interpreting omics data".
Finally, I feel it is very important to add a new category for (cross-traits) meta-analysis. A lot of reserachers would want to do this when a lot of GWAS are available. This includes the traditional MTAG software, a new PLEIO software published this year at AJHG: "a method to map and interpret pleiotropic loci with GWAS summary statistics"
Best regards, Jie