Skip to content

Instantly share code, notes, and snippets.

Avatar
🎯
Focusing

Daniel Himmelstein dhimmel

🎯
Focusing
View GitHub Profile
@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
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
View pubmed-growth.ipynb
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
@dhimmel
dhimmel / amphetamine-streams.ipynb
Last active Sep 21, 2016
How much Baltimore stream water do you need to drink to get high?
View amphetamine-streams.ipynb
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
@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 / 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 / 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
View IRKernel-less-than-bug.ipynb
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
@dhimmel
dhimmel / OPC-differentiation-DEGs.tsv
Last active Mar 1, 2016
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.
View OPC-differentiation-DEGs.tsv
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
dhimmel / ije-blog-post.md
Last active Mar 14, 2016
GWAS births a new breed of disease network
View ije-blog-post.md

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.


Genome-wide association study gives rise to a new breed of disease network

By Daniel Himmelstein

A puzzling similarity