Medical Research Council Biostatistics Unit at the University of Cambridge's repositories
real-time-mcmc
MCMC version of the UKHSA/Cambridge real-time model for epidemic surveillance. Forked on 29/08/2023 but not kept up to date - for the latest version, see https://gitlab.com/pjbirrell/real-time-mcmc , and for background information see https://royalsocietypublishing.org/doi/full/10.1098/rstb.2020.0279
BASiCS
BASiCS: Bayesian Analysis of Single-Cell Sequencing Data. This is an unstable experimental version. Please see http://bioconductor.org/packages/BASiCS/ for the official release version (forked to the unit's github)
coloc
Repo for the R package coloc (forked to the unit's github)
DGP4LCF
Model high-dimensional gene expression trajectories using dynamic factor analysis with dependent Gaussian processes (forked from https://github.com/jcai-1122/DGP4LCF)
DRMR
Doubly-Ranked Stratification in Mendelian Randomization
msm
The msm R package for continuous-time multi-state modelling of panel data (forked to the unit's github)
SUMnlmr
non-linear MR for semi-summarized data
atlasqtl
atlasqtl R package - Fast global-local hotspot QTL detection (forked to the unit's github)
batchmix
Semi-supervised and unsupervised Bayesian mixture models that simultaneously infer the cluster/class structure and a batch correction. Densities available are the multivariate normal and the multivariate t. The model sampler is implemented in C++. This package is aimed at analysis of low-dimensional data generated across several batches. See [Coleman et al., 2022](https://doi.org/10.1101/2022.01.14.476352) for details of the model. This version forked to the MRC-BSU github.
con-cis-MR
R code to implement the methods in 'Conditional inference in cis-MR using weak genetic factors'
curtailment
Finds binary outcome trial designs using stochastic curtailment (forked to the unit's github).
epispot
epispot R package - Annotation-driven approach for large-scale joint regression with multiple responses (forked to the unit's github)
flexsurv-dev
The flexsurv R package for flexible parametric survival and multi-state modelling (forked to the unit's github)
focused-MR
R code to reproduce results of data examples in 'Selecting invalid instruments to improve MR with two-sample summary data''
Landmarking
Forked to the MRC-BSU website.
locus
locus R package - Large-scale variational inference for variable selection in sparse multiple-response regression (forked to the unit's github)
MDIr
R package for Bayesian mixture models and Multiple Dataset Integration, an extrapolation of mixture models to the multiple dataset context (mirrored from the original at https://github.com/stcolema/mdir)
navigm
The navigm implements variable-guided network inference using Bayesian graphical spike-and-slab modelling.
NeuralSurvivalClustering
Implementation for the paper Neural Survival Clustering: Non parametric mixture of neural networks for survival clustering
nlmr
Non-linear Mendelian randomization
onlineFDR
Clone of the Bioconductor repository for the onlineFDR package. See https://bioconductor.org/packages/devel/bioc/html/onlineFDR.html for the official development version, and https://dsrobertson.github.io/onlineFDR/ for easy access to documentation.
PC-GMM
R code for an application of cis-multivariable Mendelian randomization to GLP1R gene region
ProteoBayes
Bayesian toolbox for quantitative proteomics (forked from https://github.com/mariechion/ProteoBayes)
survextrap
Survival Extrapolation With a Flexible Parametric Model and External Data (forked from https://github.com/chjackson/survextrap)
TrialEmulation
Algorithms to conduct a Sequence of Target Trials analysis (forked from https://github.com/Causal-LDA/TrialEmulation).
voi
Methods to calculate the Expected Value of Information (forked from https://github.com/chjackson/voi/)