Alex H. Wagner, PhD ahwagner
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ahwagner
/ pubmed_date.py
Last active
September 1, 2019 22:31
A Python method for extracting the date from a PubMed article into a Pandas datetime object
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| import requests | |
| import datetime | |
| import pandas as pd | |
| from bs4 import BeautifulSoup | |
| __author__ = "Alex H. Wagner" | |
| def pandas_datetime_from_pmid(pmid): | |
| """Returns a pandas datetime object corresponding to the NCBI reported publication date for a PubMed ID (pmid)""" |
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ahwagner
/ Identifying Gene Categories from Guide To Pharmacology.ipynb
Created
November 19, 2016 19:31
Guide To Pharmacology Gene Categories
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ahwagner
/ preprocess.R
Last active
July 21, 2017 21:26
regularization and batch correction of samples run through cufflinks, followed by GMM annotation of genes and plotting with pheatmap
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| source("https://bioconductor.org/biocLite.R") | |
| # biocLite("sva") | |
| # biocLite("ballgown") | |
| library(ballgown) | |
| library(sva) | |
| library(pheatmap) | |
| library(mixtools) | |
| # Extract expression estimates | |
| # data_directory = "/some/data/dir" |
ahwagner
/ civic_pmids.ipynb
Created
September 26, 2017 19:09
Jupyter Notebook for extracting all PMIDs in CIViC
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ahwagner
/ merged_hpo.ipynb
Last active
July 24, 2018 15:30
All CIViC variants with merged suggested HPO terms
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ahwagner
/ VHL Variants with ClinVar ID.ipynb
Created
September 26, 2018 01:17
civic_variant_to_clinvar
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ahwagner
/ cam_evidence.ipynb
Created
April 3, 2020 21:58
Get all evidence submitted by CIViC user Cam Grisdale
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