ukbiobank

There are 1 repository under ukbiobank topic.

• OxWearables / biobankAccelerometerAnalysis

  Extracting meaningful health information from large accelerometer datasets

  actigraphactivity-trackeraxivityfitness-trackergeneactivmachine-learningukbiobank
  Language:Python 164

• dnanexus / UKB_RAP

  Access share reviewed code & Jupyter Notebooks for use on the UK Biobank (UKBB) Research Application Platform. Includes resources from DNAnexus webinars, online trainings and workshops.

  ukbiobankwdlgwas
  Language:Jupyter Notebook 99

• spiros / tofu

  Tofu is a Python tool for generating synthetic UK Biobank data.

  ukbiobanksynthetic-data
  Language:Python 51

• sarslancs / graph_saliency_maps

  Graph saliency maps through spectral convolutional networks for brain mapping

  brain-imagingdeep-learningneuroscienceresting-state-fmriukbiobank
  Language:Python 31

• Nealelab / UKBB_ldsc

  Sample code for ldsc analyses in UKBB

  heritabilityldscoreukbiobank
  Language:CSS 25

• OxWearables / actipy

  Python Software Development Kit (SDK) to process Axivity, GENEActiv, and Actigraph files

  fitness-trackeractivity-trackeraxivitygeneactivactigraphukbiobank
  Language:Python 18

• spiros / ukb-biomarker-phenotypes

  Phenotyping algorithms for common biomarkers in primary care EHR for UK Biobank

  ukbiobankehrehr-phenotypes
  18
• snpnet

  rivas-lab / snpnet

  snpnet - Efficient Lasso Solver for Large-scale genetic variant data

  statistical-learninglassopredictiongeneticsbiobanksnpnet-coxcox-regressionsparselinear-regressionsurvival-analysisukbiobankelastic-net-regression
  Language:R 17

• yeyixuan / UKBCaseFinder

  A tool for identifying patients in UK biobank given the definition of disease phenotypes (icd10, icd9, opcs or cancer histology).

  ukbiobanktoolcase-identify
  Language:R 15

• thbuerg / NeuralCVD

  🫀 Code for "Neural network-based integration of polygenic and clinical information: Development and validation of a prediction model for 10 year risk of major adverse cardiac events in the UK Biobank cohort" 🫀

  pytorch-lightningpytorchtime-to-eventsurvival-analysisukbiobankcardiovascular-diseaserisk-modeling
  Language:Jupyter Notebook 11

• tjiagoM / gtex-transcriptome-modelling

  Multilayer modelling of the human transcriptome and biological mechanisms of complex diseases and traits

  papergtextranscriptometcgaukbiobankmultilayer-networkvaepythonumaptwas
  Language:Jupyter Notebook 10

• luyang-ai4med / POPDx

  Python implementation of POPDx - Predictions for unseen, rare, and common labels.

  deep-learningphenotyping-algorithmsukbiobank
  Language:Python 9

• neurodatascience / ukbm

  Data management helper code for the UK Biobank.

  bidsukbukbiobankdata-management
  Language:Shell 8

• steno-aarhus / ukbAid

  Aid Steno Researchers Who Work on the UKB RAP.

  data-extractiondata-importreproducibilityukbiobank
  Language:R 8

• nimh-dsst / dataset-phenotypes

  Preparatory scripts for BIDS tabular phenotypic data in large neuroimaging datasets.

  bidsdata-dictionarydatasetdatasetsphenotypeabcdabidehbnhcpphenotypicpncukbukbbukbiobanknkiabcd-studyabide-datatabulartabular-data
  Language:Python 7

• dlcgold / muPBWT

  A PBWT-based light index for UK Biobank scale genotype data.

  1000genomespbwtrun-length-encodingukbiobank
  Language:C++ 6
• mvpmm

  rivas-lab / mvpmm

  MultiVariate Polygenic Mixture Model

  modelinggeneticsstatisticsukbiobankgwas-summary-statisticsmixture-modelstanbayesian-methodsgenetic-correlationsheritability
  Language:R 6

• niekverw / ukpheno

  Create binary traits for UKbio using ICD/OPER/medication/self reports/age of diagnosis/visit-dates etc). The current output includes variables on history, study visit, future, time-to-first-event, episode-duration. this is a starting point to construct your favorite trait in ukb. The code was written on the go, so not super clean code..

  ukbiobankphenotype-predictionicd-10icd-9ruk-biobank
  Language:R 4

• rivas-lab / ukbb-tools

  Tools for preprocessing, QC, and preliminary analyses from raw UK BioBank data

  ukbiobankgwasgwas-summary-statisticsgrmld-score-regressionphewasphenotyping-algorithmsglobal-biobank-engine
  Language:Jupyter Notebook 4

• tjiagoM / adni_phenotypes

  Identifying healthy individuals with Alzheimer neuroimaging phenotypes in the UK Biobank

  adnialzheimer-disease-predictionmcdropoutmrinaccukbiobank
  Language:Python 4

• jlc-christie / axivity-ax3-tool

  Command line tool written in c++ for easily extracting light and temperature data from Axivity AX3 accelerometers used in the UKBiobank

  cplusplus-11axivityax3ukbiobankbiobank
  Language:C++ 3

• vforget / ukb

  UK Biobank Tools

  ukbiobankbioinformaticsawkdata-science
  Language:Awk 3

• GuLinLin / PIXANT

  Rapid and accurate multi-phenotype imputation for millions of individuals

  bioinformaticsgenome-wide-association-studiesmachine-learningmulti-phenotype-imputationukbiobank
  2
• degas-risk

  rivas-lab / degas-risk

  Polygenic risk modeling with latent trait-related genetic components

  polygenic-risk-scoresprsukbiobankprincipal-component-analysisrisk-scoresgeneticsgwasgwas-summary-statistics
  Language:Jupyter Notebook 2

• roshchupkin / pybgen

  Light and fast pure python parser for bgen format (v.1.1; 1.2; 1.3)

  pythonbgengwasukbbukbiobankparserbioinformatics
  Language:Python 2

• carbocation / bgen

  BGEN file format reader for parsing UK Biobank and other genotype data in Go

  golanggenomicsbgenukbiobank
  Language:Go 1

• ivychad / Physical-Activity-BrainAGE

  Code for BrainAGE computation from UKBiobank T1 MRI data and further preprocessing and analysis of accelerometer-measured and self-reported physical activity and fitness data in relationship with BrainAGE..

  brainagefitnessphysical-activityukbiobank
  Language:Jupyter Notebook 1

• RajLabMSSM / echoLD

  echoverse module: LD downloading and processing

  echoverselinkage-disequilibriumgenomicsukbiobank1000genomes
  Language:R 1

• adRn-s / ukbbgwas

  Explore SNVs associated with any of UK BioBank Phenotypes, results were made publicly available by: http://www.nealelab.is/uk-biobank

  rgwas-summary-statisticsukbiobankmanhattan-plotmendelian-randomization
  Language:R 0

• rivas-lab / ANGPTL7

  Rare protein-altering variants in ANGPTL7 lower intraocular pressure and protect against glaucoma

  glaucomageneticsangptl7protectiontherapeuticsintraocular-pressureiopfinlandfinngenukbiobank
  Language:Jupyter Notebook 0

• rmgpanw / codemapper

  An R package for working with clinical codes

  rpackageukbiobank
  Language:R 0

• tomversluys / Health-consequences-of-human-mating-patterns

  This repository contains the code required to perform the data processing and analysis associated with the manuscript submitted to Nature under the name "Maladaptive Genetic Assortment in Humans

  bioinformaticsfertilitygeneralized-additive-modelsmating-systemsrukbiobank
  Language:R 0

• brainhack-school2020 / hannahkiesow_RiskyBrain

  Predicting risky behavior in structural brain volume using the UK Biobank

  atlasesfeature-engineeringmachine-learningmri-brainneurosciencenilearnstucturalukbiobankvisualization
  Language:Python

• TemryL / UKB-Tools

  Tools in Python to quickly start using the UK-BioBank dataset before UKB RAP.

  biobank-datadataprocessingpythonukbiobank
  Language:Python