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
/ 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
/ IRKernel-less-than-bug.ipynb
Last active
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
/ OPC-differentiation-DEGs.tsv
Last active
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
/ ije-blog-post.md
Last active
March 14, 2016 16:12
GWAS births a new breed of disease network
dhimmel
/ hetio-ind.adoc
Last active
January 31, 2016 21:43
2016 GraphGist Challenge · Drug repurposing by hetnet relationship prediction: a new hope · http://portal.graphgist.org/graph_gists/drug-repurposing-by-hetnet-relationship-prediction-a-new-hope
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We designed a hetnet for drug repurposing that contains 50 thousand nodes (of 10 labels) and 3 million relationships (of 27 types). And we’ve chosen neo4j for handling network storage and interaction.
I hereby claim:
- I am dhimmel on github.
- I am dhimmel (https://keybase.io/dhimmel) on keybase.
- I have a public key whose fingerprint is 8CA9 B3A5 A4B4 D442 A285 867B 03A8 B7F8 47EE A45D
To claim this, I am signing this object:
dhimmel
/ weighted-r2.R
Last active
September 5, 2022 06:03
Computing the R-squared of a linear regression model with weighted observations in R
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| # Compare four methods for computing the R-squared (R2, coefficient of determination) | |
| # with wieghted observations for a linear regression model in R. | |
| # This work was written by Daniel Himmelstein (@dhimmel) with guidance | |
| # from Alex Pankov (@a-pankov). It is released as CC0 (public domain). | |
| get_r2_cor <- function(y, y_pred, w) { | |
| # Calculate R2 using the correlation coefficient method | |
| xy = cbind(y, y_pred) | |
| return(boot::corr(d=xy, w=w) ^ 2) | |
| } |
dhimmel
/ bto-terms-in-gnf.tsv
Created
June 19, 2015 22:05
BTO (BRENDA Tissue Ontology) terms corresponding to GNF expression atlas tissues
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| bto_id | bto_name | cell_line | |
|---|---|---|---|
| BTO:0000038 | SW-480 cell | 1 | |
| BTO:0000041 | medulla oblongata | 0 | |
| BTO:0000045 | adrenal cortex | 0 | |
| BTO:0000047 | adrenal gland | 0 | |
| BTO:0000084 | vermiform appendix | 0 | |
| BTO:0000089 | blood | 0 | |
| BTO:0000141 | bone marrow | 0 | |
| BTO:0000142 | brain | 0 | |
| BTO:0000211 | caudate nucleus | 0 |