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stephens999
ashr:Methods for Adaptive Shrinkage, using Empirical Bayes
The R package 'ashr' implements an Empirical Bayes approach for large-scale hypothesis testing and false discovery rate (FDR) estimation based on the methods proposed in M. Stephens, 2016, "False discovery rates: a new deal", <DOI:10.1093/biostatistics/kxw041>. These methods can be applied whenever two sets of summary statistics---estimated effects and standard errors---are available, just as 'qvalue' can be applied to previously computed p-values. Two main interfaces are provided: ash(), which is more user-friendly; and ash.workhorse(), which has more options and is geared toward advanced users. The ash() and ash.workhorse() also provides a flexible modeling interface that can accommodate a variety of likelihoods (e.g., normal, Poisson) and mixture priors (e.g., uniform, normal).
Maintained by Peter Carbonetto. Last updated 11 months ago.
82 stars 12.10 score 780 scripts 15 dependents
psolymos
bSims:Agent-Based Bird Point Count Simulator
A highly scientific and utterly addictive bird point count simulator to test statistical assumptions, aid survey design, and have fun while doing it (Solymos 2024 <doi:10.1007/s42977-023-00183-2>). The simulations follow time-removal and distance sampling models based on Matsuoka et al. (2012) <doi:10.1525/auk.2012.11190>, Solymos et al. (2013) <doi:10.1111/2041-210X.12106>, and Solymos et al. (2018) <doi:10.1650/CONDOR-18-32.1>, and sound attenuation experiments by Yip et al. (2017) <doi:10.1650/CONDOR-16-93.1>.
Maintained by Peter Solymos. Last updated 11 months ago.
biasbirdsdetectabilityshinysimulationsurvey-design
4 stars 5.36 score 38 scripts
bioc
EGAD:Extending guilt by association by degree
The package implements a series of highly efficient tools to calculate functional properties of networks based on guilt by association methods.
Maintained by Sara Ballouz. Last updated 5 months ago.
softwarefunctionalgenomicssystemsbiologygenepredictionfunctionalpredictionnetworkenrichmentgraphandnetworknetwork
4.92 score 83 scripts