Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

Ryan R. Wick, Louise M. Judd, Claire L. Gorrie, +1

PLoS Computational Biology

BioinformaticsBiologyLong Sequencing ReadsBacterial Genome AssembliesLong-read Sequencing +13

Accelerated Profile HMM Searches

Sean R. Eddy

PLoS Computational Biology

Acceleration HeuristicEngineeringMachine LearningProfile HmmsSequence Alignment +19

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

Remco Bouckaert, Joseph Heled, Denise Kühnert, +6

PLoS Computational Biology

Software MaintenanceSoftware PlatformEngineeringBeast 2Software Engineering +18

Software for Computing and Annotating Genomic Ranges

Michael Lawrence, Wolfgang Huber, Hervé Pagès, +5

PLoS Computational Biology

EngineeringAnnotated Genomic RangesBioconductor InfrastructureGeneticsGenomics +16

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

Remco Bouckaert, Timothy G. Vaughan, Joëlle Barido‐Sottani, +22

PLoS Computational Biology

Beast 2TaxonomyBiological EvolutionModel HierarchyPhylogenetics +14

MAGMA: Generalized Gene-Set Analysis of GWAS Data

Christiaan de Leeuw, Joris M. Mooij, Tom Heskes, +1

PLoS Computational Biology

mixOmics: An R package for ‘omics feature selection and multiple data integration

Florian Rohart, Benoît Gautier, Amrit Singh, +1

PLoS Computational Biology

EngineeringGenomicsMultiple Data IntegrationR PackageData Science +15

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

Paul J. McMurdie, Susan Holmes

PLoS Computational Biology

Microbial DiversityMicrobiome BiologyR PackageDysbiosisMolecular Ecology +12

Inferring Correlation Networks from Genomic Survey Data

Jonathan Friedman, Eric J. Alm

PLoS Computational Biology

EngineeringInteraction NetworkNetwork AnalysisGenomicsCorrelation Networks +21

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

Peter Eastman, Jason Swails, John D. Chodera, +10

PLoS Computational Biology

EngineeringMolecular BiologySimulationComputational ChemistryComputational Mechanics +18