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aurumpipeline

automatic-data-explorer

An R package to explore and quality check data

awesome-causality-algorithms

An index of algorithms for learning causality with data

awesome-ehr-deeplearning

Curated list of awesome papers for electronic health records(EHR) mining, machine learning, and deep learning.

big_data_cprd

My code for analysis of >250 million electronic health records. Two paper outputs: 1. O'Sullivan JW et al Temporal trends in use of tests in UK primary care, 2000-15: retrospective analysis of 250 million tests. BMJ 2018; 363 doi: https://doi.org/10.1136/bmj.k4666 https://www.bmj.com/content/363/bmj.k4666.full and 2. O'Sullivan JW. Practice variation in the use of tests in UK primary care: a retrospective analysis of 16 million tests performed over 3.3 million patient years in 2015/16. BMC Medicine (Forthcoming)

cds

Causal Inference using Deep Bayesian Dynamic Survival Models

cleancprd

Code used to setup the CPRD data prior to the analyses conducted in the DementiaDrugsCPRD and repurposing-antihypertensives-dementia repositories.

cleanehr

Essential tools and utility functions to facilitate the data processing pipeline, data cleaning and data analysing of clinical data from CC-HIC

cmd_multimorbidity

Common mental disorders and additional long-term conditions

cprd-gold-migrant-phenotype-validation

Code, codelists and ONS datasets used for the CPRD GOLD migrant phenotype validation study

cprd-gold-migrant-primary-care-consultations

cprd-gold-migrant-sexual-and-reproductive-health-and-rights

Phenotypes and code used for analyses of sexual and reproductive health and rights (SRHR) outcomes in CPRD GOLD comparing migrants to non-migrants

cprd-lra

Code for an analysis of the association of lipid regulating agents (e.g. statins) with incidence of dementia outcomes

cprd_copd_analysis

This is the R code used to analyse the data for paper "Opportunities to reduce antibiotic prescribing for patients with COPD in primary care"

cprd_hes_variability

cprd_multimorbidity_codelists

cprd_multimorbidity_trends

data-quality-checker

Check the basic quality of any dataset

data-wrangling-functions

Functions used for wrangling education research data

deepipw

Code for paper "A deep learning framework for drug repurposing via emulating clinical trials on real world patient data" (Accepted to Nature Machine Intelligence).

dofiles

CPRD Project Incretin and CVD: Primary Outcomes

drugprepr

An algorithm for the transparent and efficient preparation of CPRD drug data into information on individuals’ drug use over time

electronic-health-records-analysis-for-sepsis

MIMIC-III(Medical Information Mart for Intensive Care III) dataset and PIC(Paediatric Intensive Care) dataset Analysis for Sepsis Management.

emogg

:chart_with_upwards_trend::heart_eyes_cat: Emoji in ggplot2 :heart_eyes_cat::chart_with_upwards_trend:

fiddle

FlexIble Data-Driven pipeLinE – a preprocessing pipeline that transforms structured EHR data into feature vectors to be used with ML algorithms. https://doi.org/10.1093/jamia/ocaa139

frustration-one-year-with-r

An extremely long review of R.

hdruk_summerschool_session_1_2

Docker image for first two sessions at the HDRUK summer school 2019

mirtazapinesafetyanalysis

Stata do-files for preparation and analysis of CPRD data for a project about the safety of mirtazapine

multimorbidityclusterscprd-gold

The nature of clusters of multimorbid patients in the UK: a latent class analysis

pdswr2

Code, Data, and Examples for Practical Data Science with R 2nd edition (Nina Zumel and John Mount) https://github.com/WinVector/PDSwR2