User: johnS

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johnS10
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Posts by johnS

<prev • 8 results • page 1 of 1 • next >
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Comment: C: Where did first Manhattan plot appear
... Looks like you got it right dsull ...
written 10 months ago by johnS10
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Comment: C: Where did first Manhattan plot appear
... Here is the manual that I was able to find which released in March 2005 where they call it Manhattan plot http://jjwanglab.org/gwasrap/static/images/gwasrank/user_manual.pdf But I am assuming if it need to be there in a manual, it should be mentioned somewhere in 2004. I am pretty new to the field. ...
written 10 months ago by johnS10
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Where did first Manhattan plot appear
... Hello Friends- Just out of curiosity where or in which paper did the first Manhattan plot appear? The first GWAS project paper got published here "Initial sequencing and analysis of the human genome" in nature genetics in 2001. And later around 2004 Manhattan plot became popular. But can't spot i ...
gwas manhattan plot written 10 months ago by johnS10
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Understanding sickle cell trait
... I am new to genomic world, so my questions might be bit silly. I been reading about it a lot recently and still I get confused with few things. And I feel if I am able to find answer for this, then I will be able to relate things. The sickle cell anemia is what I took as an example Here is my und ...
genome gene alleles rna-seq snp written 21 months ago by johnS10 • updated 21 months ago by Asaf8.5k
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How plink calculates meta-analysis
... I am trying to find the logic/calculation what is used in plink to calculate the meta analysis when run the following command plink --meta-analysis study1.assoc study2.assoc study3.assoc I checked the plink website but dint find details http://zzz.bwh.harvard.edu/plink/metaanal.shtml . Could someo ...
gwama metal meta-analysis plink written 2.1 years ago by johnS10 • updated 2.0 years ago by Biostar ♦♦ 20
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Comment: C: How to retrieve Gene name from SNP ID using biomaRt
... @kevin Blighe Thank you :-) May I know why ENSG00000143921 got ABCG8 and ABCG5,ABCG8 ? In gsnpense its only ABCG8 ...
written 2.2 years ago by johnS10
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Comment: C: How to retrieve Gene name from SNP ID using biomaRt
... @kevin Blighe Thank you. I tried it for this for snp rs6544713 getBM(attributes=c( "ensembl_gene_stable_id"), filters="snp_filter", values="rs6544713", mart=ensembl, uniqueRows=TRUE) But this is giving me only the Ensembl gene ID-s, If I lookup for the same SNP in https://biit.cs.ut.ee/gsnpe ...
written 2.2 years ago by johnS10
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How to retrieve Gene name from SNP ID using biomaRt
... I am trying to get gene name from the SNP ID, I came across some posts and came up with this, but I am getting an error Here is my code library(biomaRt) ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl") getBM(attributes = c("external_gene_name"), filters = "snp_fil ...
gene R biomart rsid snp written 2.2 years ago by johnS10 • updated 2.2 years ago by Kevin Blighe67k

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Popular Question 9 months ago, created a question with more than 1,000 views. For How to retrieve Gene name from SNP ID using biomaRt
Popular Question 21 months ago, created a question with more than 1,000 views. For How to retrieve Gene name from SNP ID using biomaRt

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