Comments (4)
Later: show best phenos in gene tooltip
Maybe when people hover over a gene, the other phenotypes should go in the tooltip. How do I make that happen? I'm sure LocusZoom's chain mechanism can support it, but I don't understand that.
from pheweb.
Choosing a region for each gene
When a user searches for a gene, what region should be shown? Just the gene plus max(200bp, 5%)
up and downstream? Sarah says that the ideal region varies by gene. If there's a peak near a gene, it might be good to extend the gene's region to capture that peak.
In that case, I would start with a wide region around a gene. Then I would get the (best_hit_pval, best_hit_pos) for each phenotype. Then I would narrow the region to just barely contain both the gene and all best_hit_pos where p<1e-6.
from pheweb.
Getting gene aliases
dnSNFP gets their gene aliases from http://www.genenames.org/ . I want the columns [symbol
, prev_symbol
, alias_symbol
]. I might also want ensembl_gene_id
.
The full dataset (in json) is at:
- ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/json/non_alt_loci_set.json
- ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/non_alt_loci_set.txt
From the page http://www.genenames.org/cgi-bin/statistics I can select many which type of gene I want. TODO: figure out which of those files (or maybe a few of them) I need. I can also build a custom download with only the columns I need, like http://www.genenames.org/cgi-bin/download?col=gd_app_sym&col=gd_prev_sym&col=gd_aliases&col=gd_pub_ensembl_id&status=Approved&status=Entry+Withdrawn&status_opt=2&where=&order_by=gd_app_sym_sort&format=text&limit=&hgnc_dbtag=on&submit=submit.
Let's not do any gene subsetting. Just use the table from that long URL, and merge it into our gencode genes as aliases.
from pheweb.
Number of phenotypes to show
Matthew recommends showing 2-9 phenotypes, depending on their significance level, and showing the p-values beside them (perhaps with a sparkline).
from pheweb.
Related Issues (20)
- url_for in random does not allow https HOT 9
- Variants page is not displayed HOT 3
- Easier Way to Use Custom LD? HOT 6
- URI as assoc_files in pheno_list.json HOT 1
- Core features of pheweb: ref/alt, add_rsid, hg17/38 HOT 3
- stroke
- ModuleNotFoundError: No module named 'pheweb.command_line' HOT 3
- 404 not found error of phewas plot page (Pheweb with structural variants) HOT 4
- "An exception occurred" when I run the command: pheweb serve --open HOT 3
- pheweb to display multiple GWAS? HOT 1
- outdated instruction "pheweb phenolist glob-files" HOT 2
- PheWeb can display phenotype correlations generated by another tool. HOT 4
- pheweb-rg-pipeline does NOT work HOT 1
- Installation Problem HOT 7
- METSIM Pheweb Instance Not Working HOT 1
- the content of pheweb HOT 1
- Not clear when 3 parts of pheweb (executable, python scripts, huge dbSNP files) got installed HOT 1
- how to display the phenotypes in sorted order? HOT 9
- Starting `pheweb add-rsids`, Completed in 57 minutes HOT 2
- interpretation HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from pheweb.