Notice: This post has been published on the International Journal of Epidemiology's Blog. This repository contains the source for the post. The published version may contain some additional minor copyedits. Please refer to the IJE Blog for the authoritative version.
dhimmel
/ ije-blog-post.md
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March 14, 2016 16:12
GWAS births a new breed of disease network
dhimmel
/ OPC-differentiation-DEGs.tsv
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March 1, 2016 23:31
Top 50 up and 50 down-regulated genes during OPC differentiation from Dugas et al (https://doi.org/10.1523/jneurosci.2572-06.2006) mapped to human orthologs.
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| probeset | fold_change | dugas_symbol | dugas_name | platform | ensembl_id | hgnc_id | hgnc_symbol | hgnc_id_manual | hgnc_symbol_manual | |
|---|---|---|---|---|---|---|---|---|---|---|
| D28111_g_at | 119.43 | MOBP | Myelin-assoc OL basic protein | HGNC:7189 | MOBP | |||||
| K00512_at | 98.36 | MBP | Myelin basic protein | affy_rg_u34a | ENSRNOG00000016516 | HGNC:6925 | MBP | HGNC:6925 | MBP | |
| M99485_at | 97.68 | MOG | Myelin oligodendrocyte glycoprotein | affy_rg_u34a | ENSRNOG00000000775 | HGNC:7197 | MOG | HGNC:7197 | MOG | |
| rc_AI233181_at | 93.05 | ESTs, no homologies found | ||||||||
| rc_AI072770_s_at | 77.71 | PLP | Proteolipid protein | affy_rg_u34a | ENSRNOG00000002419 | HGNC:9086 | PLP1 | HGNC:9086 | PLP1 | |
| X55572_at | 71.01 | APOD | Apolipoprotein D | affy_rg_u34a | ENSRNOG00000048273 | HGNC:612 | APOD | HGNC:612 | APOD | |
| rc_AA891719_at | 66.72 | ENPP6 | Ectonuc. pyrophos./phosphodiesterase 6 | affy_rg_u34a | ENSRNOG00000009660 | HGNC:23409 | ENPP6 | HGNC:23409 | ENPP6 | |
| D88534_s_at | 60.55 | PNLIP | Pancreatic lipase | affy_rg_u34a | ENSRNOG00000017725 | HGNC:9155 | PNLIP | HGNC:9155 | PNLIP | |
| rc_AA901342_at | 49.87 | OSP | Claudin 11/OL specific protein | affy_rg_u34b | ENSRNOG00000010263 | HGNC:8514 | CLDN11 | HGNC:8514 | C |
dhimmel
/ IRKernel-less-than-bug.ipynb
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March 28, 2016 18:11
IRKernel Bug: Less than symbol (`<`) causes string truncation https://github.com/IRkernel/IRkernel/issues/286
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dhimmel
/ Cheng-Table-S2.tsv
Created
April 10, 2016 01:55
Catalog of treatments from Table S2 of Cheng et al 2014 (https://doi.org/10.1186/s13073-014-0095-1)
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| compound | disease | |
|---|---|---|
| beclometasone | acute and chronic inflammation | |
| betamethasone | acute and chronic inflammation | |
| budesonide | acute and chronic inflammation | |
| dexamethasone | acute and chronic inflammation | |
| diflorasone | acute and chronic inflammation | |
| fludroxycortide | acute and chronic inflammation | |
| flunisolide | acute and chronic inflammation | |
| fluticasone | acute and chronic inflammation | |
| hydrocortisone | acute and chronic inflammation |
dhimmel
/ gwas-association-downloaded_2016-04-10-Educational attainment.tsv
Created
April 10, 2016 22:56
GWAS Catalog associations for "Educational attainment" with p ≤ 5e-8
We can make this file beautiful and searchable if this error is corrected: It looks like row 3 should actually have 34 columns, instead of 4. in line 2.
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| DATE ADDED TO CATALOG PUBMEDID FIRST AUTHOR DATE JOURNAL LINK STUDY DISEASE/TRAIT INITIAL SAMPLE SIZE REPLICATION SAMPLE SIZE REGION CHR_ID CHR_POS REPORTED GENE(S) MAPPED_GENE UPSTREAM_GENE_ID DOWNSTREAM_GENE_ID SNP_GENE_IDS UPSTREAM_GENE_DISTANCE DOWNSTREAM_GENE_DISTANCE STRONGEST SNP-RISK ALLELE SNPS MERGED SNP_ID_CURRENT CONTEXT INTERGENIC RISK ALLELE FREQUENCY P-VALUE PVALUE_MLOG P-VALUE (TEXT) OR or BETA 95% CI (TEXT) PLATFORM [SNPS PASSING QC] CNV | |
| 2013-12-01 23722424 Rietveld CA 2013-05-30 Science www.ncbi.nlm.nih.gov/pubmed/23722424 GWAS of 126,559 individuals identifies genetic variants associated with educational attainment. Educational attainment up to 126,559 European ancestry individuals NA 2q37.2 2 236149500 GBX2 AGAP1 - LOC105373944 116987 105373944 17700 11866 rs11687170-T rs11687170 11687170 downstream_gene_variant 0 0.770 3.0000000000000004E-8 7.522878745280337 (Edu Years) 0.107 [NR]unit increase Illumina, Affymetrix, Perlegen [up to 2,321,8963] (imputed) N | |
| 2013-12-01 23722424 Rietveld CA |
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| """ | |
| This file contains python functions for automatically retreiving DOI metadata | |
| and creating bibtex references. `get_bibtex_entry(doi)` creates a bibtex entry | |
| for a DOI. It fixes a Data Cite author name parsing issue. Short DOIs are used | |
| for bibtex citation keys. | |
| Created by Daniel Himmelstein and released under CC0 1.0. | |
| """ | |
| import urllib.request |
dhimmel
/ amphetamine-streams.ipynb
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September 21, 2016 19:00
How much Baltimore stream water do you need to drink to get high?
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dhimmel
/ assignment.md
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October 21, 2016 17:33
Licensing Workshop for EPID 600. https://slides.com/dhimmel/epid600
This page describes the activity for the EPID 600 lecture on Open Data Science (slides).
At the start of this class, every pupil was asked to list 3 databases / datasets / data resources that they have used in their research. For each of these three resources (time permitting), please report via the comments below the following information:
- Is the data subject to copyright? If no, end.
- Does the resource have a license?
- If no, contact the creators and inquire whether there license that allows reuse?
- If yes, does the license allow:
dhimmel
/ CIBERSORT_license.md
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March 11, 2017 18:23
CIBERSORT License obtained in August 2016 from an unidentified trusted source.
- THE BOARD OF TRUSTEES OF THE LELAND STANFORD JUNIOR UNIVERSITY ("STANFORD") provides CIBERSORT software ("Program"), including any accompanying information, materials, or manuals, free of charge for non-commercial use only. By accepting, receiving, or using the Program, you ("RECIPIENT") agree to be bound by the terms of this agreement ("Agreement"). If you do not agree to the terms of this Agreement, then do not use the Program and promptly remove all copies of the program from your computer(s).
- RECIPIENT acknowledges that the Program is a research tool still in the development stage and that it is being supplied as is, without any accompanying services, support, or improvements from STANFORD. STANFORD makes no representations and extends no warranties of any kind, neither express nor implied.
- RECIPIENT shall not use the Program on behalf of any organization that is not a non-profit organization. RECIPIENT shall not use the Program for commercial