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ahwagner / MLL Status.ipynb
Created March 16, 2016 20:27
MLL Status.ipynb
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@ahwagner
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
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)"""
@ahwagner
ahwagner / CIViC term mapping.ipynb
Last active August 29, 2016 03:47
CIViC_term_mapping.ipynb
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@ahwagner
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
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
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
ahwagner / civic_pmids.ipynb
Created September 26, 2017 19:09
Jupyter Notebook for extracting all PMIDs in CIViC
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@ahwagner
ahwagner / merged_hpo.ipynb
Last active July 24, 2018 15:30
All CIViC variants with merged suggested HPO terms
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@ahwagner
ahwagner / VHL Variants with ClinVar ID.ipynb
Created September 26, 2018 01:17
civic_variant_to_clinvar
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@ahwagner
ahwagner / vr-spec-index.ipynb
Created July 25, 2019 20:46
Add VR index to VICC records
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@ahwagner
ahwagner / cam_evidence.ipynb
Created April 3, 2020 21:58
Get all evidence submitted by CIViC user Cam Grisdale
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