preseqR-package {preseqR}

Predicting r-species accumulation curves

Description

The functionality of this package is to predict r-species accumulaiton curves. The method is based on a nonparametric empirical Bayes approach with rational function approximation. The estimator is excellent in accuracy for both large values of r and long-range extrapolations, which are essential to large-scale applications. Some examples are predicting the molecular complexity of sequencing libraries, estimating the minimum sufficient sequencing depths for whole-exome sequencing experiments and optimizing depths for single-cell whole-genome sequencing experiments.

Details

main functions:

preseqR.rSAC

preseqR.rSAC.bootstrap

preseqR.optimal.sequencing

preseqR.rSAC.sequencing.rmdup

preseqR.sample.cov

preseqR.sample.cov.bootstrap

Author(s)

Chao Deng, Timothy Daley, and Andrew D. Smith

Maintainer: Chao Deng <[e-mail]>

References

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Daley, T., & Smith, A. D. (2013). Predicting the molecular complexity of sequencing libraries. Nature methods, 10(4), 325-327.

Deng C, Daley T & Smith AD (2015). Applications of species accumulation curves in large-scale biological data analysis. Quantitative Biology, 3(3), 135-144. URL http://dx.doi.org/10.1007/s40484-015-0049-7.

Deng, C., Daley, T., Calabrese, P., Ren, J., & Smith, A.D. (2016). Estimating the number of species to attain sufficient representation in a random sample. arXiv preprint arXiv:1607.02804v3.

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