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Daniel Himmelstein dhimmel

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dhimmel / onename.txt
Created Sep 3, 2014
onename verification
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Verifying that +dhimmel is my Bitcoin username. You can send me #bitcoin here: https://onename.io/dhimmel
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dhimmel / vtm.R
Last active Aug 29, 2015
Variable threshold metrics in R for evaluating classifier performance
View vtm.R
library(ROCR)
library(caTools)
VariableThresholdMetrics <- function(score, status) {
#' Evaluate the performance of predictions for a binary outcome.
#'
#' @param score A vector of predictions for which performance should be evalauted.
#' @param status A vector of the actual outcome: \code{0} (for negatives) and \code{1} (for positives).
#' @return A list.
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dhimmel / sung-views.ipynb
Created Jun 6, 2015
Retrieve article level metrics for a PLOS article and visualize views over time.
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@dhimmel
dhimmel / elevcan-voe.ipynb
Created Jun 16, 2015
Vibration of effects analysis for lung cancer versus elevation
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dhimmel / bto-terms-in-gnf.tsv
Created Jun 19, 2015
BTO (BRENDA Tissue Ontology) terms corresponding to GNF expression atlas tissues
View bto-terms-in-gnf.tsv
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
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dhimmel / keybase.md
Created Nov 23, 2015
Proving account ownership for keybase.io
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Keybase proof

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
dhimmel / preprints.ipynb
Last active Jan 4, 2016
Growth of bioscience preprints in 2015
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dhimmel / hetio-ind.adoc
Last active Jan 31, 2016
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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Drug repurposing by hetnet relationship prediction: a new hope


A long time ago in a galaxy far, far away…​.

@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
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dhimmel / ije-blog-post.md
Last active Mar 14, 2016
GWAS births a new breed of disease network
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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