User: joshf

gravatar for joshf
joshf20
Reputation:
20
Status:
New User
Location:
Netherlands
Last seen:
2 years, 11 months ago
Joined:
3 years, 7 months ago
Email:
j*********@gmail.com

Posts by joshf

<prev • 15 results • page 1 of 2 • next >
0
votes
2
answers
1.1k
views
2
answers
Comment: C: Why are SNPs with small effect sizes a problem for GWAS?
... No, it's not, but I'm learning about the GWAS (in this case its disadvantages) for an internship ...
written 2.9 years ago by joshf20
2
votes
2
answers
1.1k
views
2
answers
Why are SNPs with small effect sizes a problem for GWAS?
... Why does increasing a sample size increase the power for detecting SNPs with small effect sizes? ...
gwas written 2.9 years ago by joshf20 • updated 2.9 years ago by H.Hasani680
1
vote
1
answer
1.4k
views
1
answer
How to determine which SNPs are above FDR line?
... Hey so here I have an R script I use to make Q-Q plots for GWA SNP P-values with FDR lines. How could I determine with programming which P-values (or SNPs, really) are significant enough to have passed the 0.05 FDR line? I'm just really not sure how to approach this. Example below! qqunif = ...
fdr R snp gwas written 3.2 years ago by joshf20 • updated 3.2 years ago by Kolea Zimmerman80
1
vote
1
answer
3.6k
views
1
answer
Q-Q plots with GWAS p-values using R (needs confidence band)
... I'm trying to create Q-Q plots with GWAS p-values using **R** but it hasn't really been working out. I need for them to be on a -log10 scale, and for them to have a confidence band/interval. I tried out: - **qqman** - works great and it's simple but it does not provide a confidence interval func ...
q-q plots R gwas written 3.2 years ago by joshf20 • updated 8 months ago by Kevin Blighe42k
0
votes
1
answer
1.1k
views
1
answers
Comment: C: Map genes to Reactome pathways
... Ah, I see what I did wrong originally haha. I WAS completely missing something. thanks! ...
written 3.3 years ago by joshf20
1
vote
1
answer
1.1k
views
1
answer
Map genes to Reactome pathways
... I want to map a large list of genes (basically all of UCSC's known genes) to Reactome pathways. I tried using the UCSC Table Browser and it mapped a lot of the genes to pathways, but there's still a lot missing. For example, I know the gene SETD2 plays a role in R-HSA-3214841, but according to the T ...
pathway genes reactome written 3.3 years ago by joshf20 • updated 3.3 years ago by Jean-Karim Heriche18k
0
votes
2
answers
3.0k
views
2
answers
Comment: C: Map genes to KEGG pathways
... I'll give this a try, thanks! ...
written 3.6 years ago by joshf20
2
votes
2
answers
3.0k
views
2
answers
Map genes to KEGG pathways
... I have a list of ~13k genes that I need to map to KEGG pathways. I’m aware that this has sort of been asked before but I’m not so sure the answers are still up-to-date? DAVID for example hasn’t been updated since 2010. Could I still use gene2pathway or subpathwayMiner without losing a lot of inform ...
pathway gene kegg written 3.6 years ago by joshf20 • updated 2.6 years ago by EagleEye6.3k
0
votes
4
answers
20k
views
4
answers
Comment: C: Mapping Genes To Pathway
... Is it still possible to map genes to KEGG pathways using gene2pathway or SubpathwayMiner? neither have been updated in like 5 years but I'm not sure if it matters ...
written 3.6 years ago by joshf20
13
votes
5
answers
2.5k
views
5
answers
Merge 2 files based on rs number but keep all info only from the first file
... I would like to merge two files by based on one column (rs number). Not all rs numbers in file 1 are in file 2, and not all in file 2 are in file 1. However, I wanna keep ALL lines from file 1 in the output. File 1 (example): rs chr bp p rs1 chr1 729679 0.9456 rs2 chr1 731 ...
snp awk written 3.6 years ago by joshf20 • updated 3.6 years ago by Jorge Amigo11k

Latest awards to joshf

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1104 users visited in the last hour