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dhimmel / Cheng-Table-S2.tsv
Created Apr 10, 2016
Catalog of treatments from Table S2 of Cheng et al 2014 (https://doi.org/10.1186/s13073-014-0095-1)
View Cheng-Table-S2.tsv
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
dhimmel / CIBERSORT_license.md
Last active Mar 11, 2017
CIBERSORT License obtained in August 2016 from an unidentified trusted source.
View CIBERSORT_license.md

STANFORD NON-COMMERCIAL SOFTWARE LICENSE AGREEMENT

  1. 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).
  2. 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.
  3. 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
@dhimmel
dhimmel / GSEA-license.md
Last active Mar 11, 2017
GSEA/MSigDB License Agreement. Retrieved from http://software.broadinstitute.org/gsea/register.jsp?next=index.jsp on 2017-01-13
View GSEA-license.md

GSEA/MSigDB LICENSE AGREEMENT

MASSACHUSETTS INSTITUTE OF TECHNOLOGY SINGLE USER LICENSE AGREEMENT FOR INTERNAL RESEARCH PURPOSES ONLY

This Agreement is made between Massachusetts Institute of Technology with a principal address at 77 Massachusetts Avenue, Cambridge, MA 02139 ("MIT") and the subscriber above ("LICENSEE"), and is effective at the date the downloading is completed and proper registration/licensee subscriber information submitted ("EFFECTIVE DATE").

WHEREAS, LICENSEE desires to license the PROGRAM and/or DATABASE, as defined hereinafter, MIT wishes to have this PROGRAM and DATABASE utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14, and

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View assignment.md

EPID 600 Workshop

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:

  1. Is the data subject to copyright? If no, end.
  2. Does the resource have a license?
  3. If no, contact the creators and inquire whether there license that allows reuse?
  4. If yes, does the license allow:
@dhimmel
dhimmel / pubmed-growth.ipynb
Last active Oct 20, 2016
PubMed growth over time
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@dhimmel
dhimmel / amphetamine-streams.ipynb
Last active Sep 21, 2016
How much Baltimore stream water do you need to drink to get high?
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@dhimmel
dhimmel / autobib.py
Created Apr 29, 2016
Automatically create BibTeX entries from DOIs
View autobib.py
"""
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
dhimmel / gwas-association-downloaded_2016-04-10-Educational attainment.tsv
Created Apr 10, 2016
GWAS Catalog associations for "Educational attainment" with p ≤ 5e-8
View gwas-association-downloaded_2016-04-10-Educational attainment.tsv
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.
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
@dhimmel
dhimmel / IRKernel-less-than-bug.ipynb
Last active Mar 28, 2016
IRKernel Bug: Less than symbol (`<`) causes string truncation https://github.com/IRkernel/IRkernel/issues/286
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