Alternatives and similar repositories for pyPheWAS:

Users that are interested in pyPheWAS are comparing it to the libraries listed below

• celehs / PheCAP
  https://celehs.github.io/PheCAP/
  ☆21Updated 3 years ago
• saphir746 / BiobankRead-Bash
  Python scripts to extract and pre-process UKB data
  ☆31Updated 5 years ago
• spiros / ukb-biomarker-phenotypes
  Phenotyping algorithms for common biomarkers in primary care EHR for UK Biobank
  ☆24Updated 4 years ago
• RuishanLiu / TrialPathfinder
  ☆61Updated 3 years ago
• nadavbra / ukbb_parser
  A Python module for loading phenotypic and genetic data from the UK Biobank.
  ☆35Updated 3 years ago
• EHDEN / ETL-UK-Biobank
  ETL UK-Biobank
  ☆13Updated 2 years ago
• BenGlicksberg / PatientExploreR
  Dynamic visualization of Electronic Health Record data in the OMOP framework
  ☆28Updated 3 years ago
• HPIMS / phe2vec
  Phe2vec: Automated Disease Phenotyping based on Unsupervised Embeddings from Electronic Health Records
  ☆24Updated 4 years ago
• spiros / ukbiobank-resources
  A curated list for preprocessing, cleaning, mapping and analyzing UK Biobank data.
  ☆49Updated 2 years ago
• spiros / chronological-map-phenotypes
  Machine-readable version of electronic health record phenotypes for Kuan V. and Denaxas S. et al.
  ☆48Updated 10 months ago
• spiros / docker-ukbiobank-utils
  Docker image for running UK Biobank utilities: ukbunpack, ukbfetch, ukblink, ukbgene, ukbmd5, ukbconv, and gfetch
  ☆12Updated 3 years ago
• PhilAppleby / ukbb-srmed
  Text matching UK Biobank Self-Reported medication descriptions for medication classification
  ☆24Updated 3 years ago
• mims-harvard / Clinical-knowledge-embeddings
  Unified Clinical Vocabulary Embeddings for Advancing Precision Medicine
  ☆53Updated this week
• spiros / phemap
  Functions to map between ICD-10 terms and PheCodes for UK Biobank hospital electronic health records
  ☆34Updated 2 years ago
• bjcairns / ukbschemas
  Use R to generate a database containing the UK Biobank data schemas from http://biobank.ctsu.ox.ac.uk/crystal/schema.cgi
  ☆20Updated 4 years ago
• spiros / tofu
  Tofu is a Python tool for generating synthetic UK Biobank data.
  ☆58Updated last year
• CogStack / Foresight
  Deep Generative Modelling of Patient Timelines using Electronic Health Records
  ☆59Updated last year
• landiisotta / convae_architecture
  ☆40Updated 3 years ago
• spiros / hdr-caliber-phenotype-library
  HDR UK National Phenotype Library
  ☆22Updated 2 years ago
• bionlplab / bioc
  Data structures and code to read/write BioC XML and Json.
  ☆32Updated last year
• beamandrew / cui2vec
  ☆53Updated 5 years ago
• callahantiff / OMOP2OBO
  OMOP2OBO: A Python Library for mapping OMOP standardized clinical terminologies to Open Biomedical Ontologies
  ☆87Updated last year
• mims-harvard / SHEPHERD
  SHEPHERD: Few shot learning for phenotype-driven diagnosis of patients with rare genetic diseases
  ☆53Updated 8 months ago
• tatonetti-lab / onsides
  A resource of adverse drug effects extracted from FDA structured product labels
  ☆77Updated last week
• WGLab / EHR-Phenolyzer
  A pipeline that takes clinical notes from EHRs and generate phenotype terms, then generate ranked gene list
  ☆37Updated last year
• hakyimlab / ukbrest
  ukbREST: efficient and streamlined data access for reproducible research of large biobanks
  ☆38Updated 3 years ago
• insitro / EmbedGEM
  EmbedGEM: A framework to evaluate the utility of embeddings for genetic discovery
  ☆21Updated 7 months ago
• luyang-ai4med / POPDx
  Python implementation of POPDx - Predictions for unseen, rare, and common labels.
  ☆9Updated 10 months ago
• philipdarke / ukbb-ehr-data
  Prepare UK Biobank Electronic Health Record data for research
  ☆26Updated 2 years ago
• dfci / matchengine-V2
  Open source engine for matching cancer patients to precision medicine clinical trials (V2).
  ☆36Updated last year