Alex H. Wagner, PhD ahwagner

## Ref Allele Normalization.ipynb

      
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                ahwagner
                / Ref Allele Normalization.ipynb
            
            
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              May 11, 2020 16:10
            
              
                Workbook for testing different normalization strategies
              
          
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## cam_evidence.ipynb

      
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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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## vr-spec-index.ipynb

      
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                / vr-spec-index.ipynb
            
            
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              July 25, 2019 20:46
            
              
                Add VR index to VICC records
              
          
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## VHL Variants with ClinVar ID.ipynb

      
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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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## merged_hpo.ipynb

      
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                ahwagner
                / merged_hpo.ipynb
            
            
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              July 24, 2018 15:30
            
              
                All CIViC variants with merged suggested HPO terms
              
          
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## civic_pmids.ipynb

      
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                ahwagner
                / civic_pmids.ipynb
            
            
              Created
              September 26, 2017 19:09
            
              
                Jupyter Notebook for extracting all PMIDs in CIViC
              
          
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## preprocess.R
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"

## Identifying Gene Categories from Guide To Pharmacology.ipynb

      
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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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## CIViC term mapping.ipynb

      
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                ahwagner
                / CIViC term mapping.ipynb
            
            
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              August 29, 2016 03:47
            
              
                CIViC_term_mapping.ipynb
              
          
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## pubmed_date.py
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)"""
	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"
	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)"""