Daniel W. Schafer

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GENE-counter is a complete Perl-based computational pipeline for analyzing RNA-Sequencing (RNA-Seq) data for differential gene expression. In addition to its use in studying transcriptomes of eukaryotic model organisms, GENE-counter is applicable for prokaryotes and non-model organisms without an available genome reference sequence. For alignments,(More)
Exposure assessment poses special problems in air pollution epidemiology. This paper proposes a probit regression model for binary and ordinal outcomes that uses exposure validation information to develop estimates for the coefficient of the true exposure when only the inaccurate 'surrogate' measure of exposure is available for the individuals in the health(More)
This article demonstrates semiparametric maximum likelihood estimation of a nonlinear growth model for fish lengths using imprecisely measured ages. Data on the species corvina reina, found in the Gulf of Nicoya, Costa Rica, consist of lengths and imprecise ages for 168 fish and precise ages for a subset of 16 fish. The statistical problem may therefore be(More)
The performance of 3426 subjects on 100-word lists from Northwestern University Auditory Test #6 was analyzed to determine the application of a binomial model previously suggested by Thornton and Raffin (1978). It was found that the critical differences based on this model can be used to describe accurately the variability associated with(More)
This work is about assessing model adequacy for negative binomial (NB) regression, particularly (1) assessing the adequacy of the NB assumption, and (2) assessing the appropriateness of models for NB dispersion parameters. Tools for the first are appropriate for NB regression generally; those for the second are primarily intended for RNA sequencing(More)
RNA sequencing (RNA-Seq) is the current method of choice for characterizing transcriptomes and quantifying gene expression changes. This next generation sequencing-based method provides unprecedented depth and resolution. The negative binomial (NB) probability distribution has been shown to be a useful model for frequencies of mapped RNA-Seq reads and(More)
Index 197 Sleuth3-package The R Sleuth3 package Description Data sets from Ramsey and Schafer's "Statistical Sleuth (3rd ed)" Details This package contains a variety of datasets. For a complete list, use library(help="Sleuth3") or Sleuth3Manual(). Maintainer: Berwin A Turlach <Berwin.Turlach@gmail.com> 6 case0101 case0101 Motivation and Creativity(More)
A 56-year-old woman displayed a condition of alternating unilateral lachrymation while she was undergoing psychotherapy. Although she was aware of this condition only since her marriage, hypnotic age regression revealed its existence in childhood, together with mutism and a catatonic trance-like state. Further investigation revealed the connection of this(More)
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