Daniel Himmelstein (@dhimmel)
github

dhimmel

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  • Stars
    star
    688
  • Global Rank 43,340 (Top 2 %)
  • Followers 411
  • Following 110
  • Registered almost 13 years ago
  • Most used languages
    Jupyter Notebook
         62.0 %
    Python
         16.0 %
    HTML
         14.0 %
    PostScript     2.0 %
    TeX
         2.0 %
    CSS
         2.0 %
    Web Ontology Language     2.0 %
  • Location 🇺🇸 United States
  • Country Total Rank 11,710
  • Country Ranking
    Web Ontology Language     6
    PostScript     183
    Jupyter Notebook
         882
    HTML
         968
    TeX
         2,808
    Python
         6,033

Top repositories

1

drugbank

User-friendly extensions of the DrugBank database
HTML
151
star
2

obonet

OBO-formatted ontologies → networkx (Python 3)
Python
127
star
3

integrate

Scripts and resources to create Hetionet v1.0, a heterogeneous network for drug repurposing
Jupyter Notebook
28
star
4

scopus

User-friendly Scopus and Journal Metrics data
Jupyter Notebook
26
star
5

hackjohn

Bot to monitor for southbound permit spaces on the John Muir Trail
Python
25
star
6

clintrials

Cataloging pharmacotherapies in clinical trial from ClinicalTrials.gov
Jupyter Notebook
23
star
7

lincs

Library of Integrated Cellular Signatures L1000
Jupyter Notebook
23
star
8

bitcoin-whitepaper

Reproducing the Bitcoin Whitepaper using the Manubot
HTML
21
star
9

disease-ontology

User-friendly extensions to the Disease Ontology
Web Ontology Language
20
star
10

plostime

Publication delays at PLOS and 3,475 other journals
19
star
11

hsdn

Analysis of the human symptoms–disease network
HTML
18
star
12

SIDER4

Processing SIDER 4.1: the side effect resource
Jupyter Notebook
18
star
13

indications

Processing high-throughput drug indication resources.
HTML
13
star
14

delays

Trends in scientific publishing delays
Jupyter Notebook
10
star
15

pubmedpy

Utilities for interacting with NCBI EUtilities relating to PubMed
Python
9
star
16

dump-actions-context

Expose GitHub actions context based on the workflow event type
9
star
17

mesh

User-friendly extensions to MeSH
Jupyter Notebook
8
star
18

bindingdb

Process BindingDB
HTML
8
star
19

disgenet

Processing the DisGeNET database of disease–gene association
Jupyter Notebook
7
star
20

snplentiful

SNP abundance correlates with network degree
Jupyter Notebook
7
star
21

biorxiv-licenses

The licensing of bioRxiv preprints
Jupyter Notebook
7
star
22

gene-ontology

User-friendly Gene Ontology annotations
Jupyter Notebook
7
star
23

fratjuice

Uncovering the microbes of fraternity basements
Python
6
star
24

rephetio

Miscellaneous Content for Project Rephetio to repurpose drugs
Jupyter Notebook
6
star
25

rephetio-manuscript

Markdown source for the Project Rephetio Manuscript https://doi.org/10.7554/eLife.26726
HTML
6
star
26

hodgkins

Human disease network based on GWAS loci
Jupyter Notebook
5
star
27

het.io-dag-data

Data backend for http://het.io/disease-genes
5
star
28

drugcentral

Converting DrugCentral data to Rephetio identifiers
Jupyter Notebook
4
star
29

uniprot

Extract uniprot mappings to other vocabularies
4
star
30

learn

Machine learning and feature extraction for the Rephetio project
Jupyter Notebook
4
star
31

psb-manuscript

Manuscript source for the People of the Pacific Symposium on Biocomputing
HTML
3
star
32

SIDER2

Calculating compound similarities using side effects and indications extracted from drug labels
TeX
3
star
33

gtex

GTEx Expression Analysis
3
star
34

entrez-gene

Processing the human Entrez Gene subset
Jupyter Notebook
3
star
35

diseases

Processing the DISEASES database
Jupyter Notebook
3
star
36

het.io-rep-data

Data from Project Rephetio for the het.io website
Jupyter Notebook
2
star
37

pathways

A compilation of pathway gene sets
Jupyter Notebook
2
star
38

elevcan

Elevation and Cancer Incidence
PostScript
2
star
39

irreproducible-timestamps

Replication analysis of Irving & Holden 2016
Jupyter Notebook
2
star
40

tissues

Gene–Tissue relationships from the TISSUES database
2
star
41

mesothelioma

Data visualization of mesothelioma in Python
Jupyter Notebook
2
star
42

ppi

Compiling human protein–protein interactions
Jupyter Notebook
2
star
43

myelinet

Hetnet prediction of candidate remyelinating compounds
Jupyter Notebook
2
star
44

bgee

Extracting anatomy-specific gene expression in humans from Bgee
Jupyter Notebook
2
star
45

stargeo

Generating expression signatures for disease using STARGEO
Jupyter Notebook
2
star
46

gwas-catalog

Extracting disease-gene associations from the GWAS Catalog
Jupyter Notebook
2
star
47

het.io-rep-guides

Neo4j Browser Guides for Project Rephetio Predictions
Jupyter Notebook
1
star
48

kg

1000 Genomes
1
star
49

doaf

Processing data from DOAF, the Disease Ontology Annotation Framework
Jupyter Notebook
1
star
50

unichem

A python package for mapping compounds via UniChem
Python
1
star
51

covid-publication-times

COVID-19 Literature Publication Times
Jupyter Notebook
1
star
52

advent-of-code

Advent Of Code 2021
Python
1
star
53

erc

Processing human Evolutionary Rate Covariation data
Jupyter Notebook
1
star
54

2011-ucsf-bp205a-microarray-project

A set of python utilities for analyzing microarray data.
Python
1
star
55

uberon

User-friendly anatomical structures data from the Uberon Ontology
Jupyter Notebook
1
star
56

code-96

Testing repo for https://github.com/greenelab/manubot-rootstock/pull/101
CSS
1
star
57

het.io-dag-pycode

Python Code for Hetio Disease-Gene Prediction Study (PLOS Comp Bio, 2015)
Python
1
star