New blog!
I will no longer be posting to this blog, instead I will be using http://mlbernauer.bitbucket.org/
Data Cleansing: FDA Adverse Event Reporting System
Many data sets are inherently dirty, they contain misspellings, missing data, erroneous values, etc. This is particularly true for data sets created by people typing information into forms or spreadsheets […]
FDA Adverse Event Reporting System
I’ve been collecting FDA Adverse Event Reporting (FAERS) data for quite some time now in hopes of using it in various pharmacovigilance projects. The FDA makes this data available to […]
US Colleges of Pharmacy
A collection of US colleges of pharmacy created by scraping the U.S. News Best Grad Schools list. CSV
Entrez: An R package for retrieving and parsing results from NCBI
Recently, I created a few R functions for querying and retrieving results from NCBI using E-utilities. Instead of copying these functions into my working directory each time I wanted to […]
Entrez E-Utilities API and R
Note: Source code can be obtained here I’ve posted on using PubMed as a resource for text analysis before (here and here). For those projects I would download PubMed results […]
UNM College of Pharmacy Research Collaborations
I was interested in seeing what institutions frequently collaborate with researchers from UNM College of Pharmacy. Using PubMed publication records I was able to create the figure below which shows […]
UNM College of Pharmacy Publications
PubMed is a fantastic database for biomedical literature and contains over 24.4 million entries to date. One of PubMed’s greatest features is it’s ability to allow users to create custom […]
Text Mining PubMed: Parsing Medline Files in R
NOTE: The source code for the R module can be found here I often use the Medline module from the Biopython library for parsing and extracting data from PubMed Medline […]
Statistical Method for Automated Cell Detection and Counting
NOTE: The IPython notebook used in this project can be found here. Introduction: I used to work in a cancer lab at Lovelace Respiratory Research Institute where one of my […]
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