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Found 4 papers, 3 papers with code
The Canadian VirusSeq Data Portal & Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology
The COVID-19 pandemic led to a large global effort to sequence SARS-CoV-2 genomes from patient samples to track viral evolution and inform public health response.
Generalized Functional Pruning Optimal Partitioning (GFPOP) for Constrained Changepoint Detection in Genomic Data
We describe a new algorithm and R package for peak detection in genomic data sets using constrained changepoint algorithms.
Computation
A log-linear time algorithm for constrained changepoint detection
This leads to a new algorithm which can solve problems with arbitrary affine constraints on adjacent segment means, and which has empirical time complexity that is log-linear in the amount of data.
PeakSegJoint: fast supervised peak detection via joint segmentation of multiple count data samples
To select the number of peaks in the segmentation, we propose a supervised penalty learning model.
