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Advanced features7 months ago
Life expectancy in the US | Operating within the loop | Using ith_step() with multiple chains | Saving information as it happens
Extending partition2 years ago
Customizing existing partitioners | Creating new partitioners | partition_step(), map_cluster(), and reduce_cluster()
Introduction to Partition2 years ago
Introduction to the partition package | Reducing data with partition | The partition algorithm | Direct-Measure-Reduce and Partitioners | Permutation tests | References
Getting Started with slurmR3 years ago
The slurmR R package | Socket clusters | Job arrays using the *apply family | Sockets vs Arrays | Example simulating Pi | Single node (machine), multi-core simulation | Multi-job submission with job arrays | Multi-node cluster object
LUCIDus: an R package to implement integrative clustering4 years ago
Introduction | Introduction to the LUCID model | General workflow | Fit LUCID model | Interpreting LUCID model | Visualization of LUCID | Regularization | Model selection | Inference | Incorporating missing omics data
Simulation and Inference5 years ago
Setup | Simulation | Inference
Working with Slurm5 years ago
Introduction | Definitions | Submitting jobs via sbatch
Workflow with fmcmc5 years ago
Motivating example | Reusing fmcmc_kernel objects | Accessing other elements of the chain
User-defined kernels5 years ago
Introduction | Size parameter in a binomial distribution
Re-submission and debugging5 years ago
Introduction | Checking logs | Job-resubmission
hJAM Vignette5 years ago
Overview | Implementation | General input | Get conditional $\hat{A}$ matrix | Example | Data exploration | Conversion of $\hat{A}$ matrix | hJAM | Conclusion
selectKSigs: a package for selecting the number of mutational signatures7 years ago
Introduction | Paper | Installing and loading the package | Installation | Bioconductor | Input data | Mutation Position Format | Workflow | Get input data | Perform the selecting process | Visualizing the results | Session info
HiLDA: a package for testing the burdens of mutational signatures7 years ago
Introduction | Paper | Installing and loading the package | Installation | Bioconductor | Just Another Gibbs Sampler (JAGS) | Input data | Mutation Position Format | Workflow | Get input data | Run tests from HiLDA | Perform the global test and the local test | Get signatures from pmsignature | Perform the global test and the local test with initial values | Assess Convergence of MCMC chains | Visualize the mutation signatures from pmsignature | Visualize the mutation signatures from HiLDA | Output the posterior distribution of the mean difference in exposures