Johns Hopkins Precision Medicine Analytics Platform (PMAP) Cookbook
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About the PMAP Cookbook
Table of Contents
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Before you start cooking
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Do you need an IRB to acccess PMAP
What type of protocol should I submit for my research use of PMAP?
Do I have to get Data Trust approval to use PMAP?
How can I tell what data are available in PMAP?
Intro to Crunchr and Jupyter Notebooks
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Crunchr collaborative data science platform
How to access the PMAP Cookbook on Crunchr
Steps to using Crunchr for collaborative research
Introduction to Jupyter notebooks
How to access files from your Johns Hopkins H: drive
How to access files from your Johns Hopkins S: drive
Accessing Your Data
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Accessing your data through Python
Accessing your data through RStudio
Accessing your data with Stata
Working with EMR Data (Python)
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Connecting to the PMAP database server
Requesting access to the asthma dataset
Intro to SQL for mining EMR data
Ashthma cohort discovery with regular expressions and set operators
Exploratory data analysis and visualization of EMR data
Data cleaning example
Data quality assessment example
Statistical testing EMR Asthma example
Conducting NLP Projects (Python)
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Tokenizing a corpus of text
Matching text with Regular Expression
ngrams and term weighting
Document classification
Working with Medical Images (Python)
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How to Access DICOMs From XNAT
Working with DICOM image files
Radiomics Example
High Perfomance Compute (HPC) clusters for Image Analysis
Hello World Chest X-Ray Deep learning example
Programming Resources
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Python Data Science Handbook
(O'Reilly Media)
Python programming
Data Manipulation with Pandas
Data Visualization with Matplotlib
Introduction to Numpy
Machine Learning with Scikit
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