Search results for "Software"
showing 10 items of 7396 documents
Multiple testing of pairs of one-sided hypotheses
1986
Two-sided test procedures fork real parameters should point out in the case of rejection whether the left or the right alternative can be assumed. This sets up a multiple testing problem fork pairs of one-sided hypotheses. Holm's (1979, Scandinavian Journal of Statistics 6:65–70) sequentially rejective test provides a solution the critical levels of which are slightly improved. Considerable improvement is obtained when the hypotheses are redefined to be disjoint in pairs.
An overview of robust Bayesian analysis
1994
Robust Bayesian analysis is the study of the sensitivity of Bayesian answers to uncertain inputs. This paper seeks to provide an overview of the subject, one that is accessible to statisticians outside the field. Recent developments in the area are also reviewed, though with very uneven emphasis. © 1994 SEIO.
A new mathematical approach for the estimation of the AUC and its variability under different experimental designs in preclinical studies
2011
The aim of the present work was to develop a new mathematical method for estimating the area under the curve (AUC) and its variability that could be applied in different preclinical experimental designs and amenable to be implemented in standard calculation worksheets. In order to assess the usefulness of the new approach, different experimental scenarios were studied and the results were compared with those obtained with commonly used software: WinNonlin® and Phoenix WinNonlin®. The results do not show statistical differences among the AUC values obtained by both procedures, but the new method appears to be a better estimator of the AUC standard error, measured as the coverage of 95% confi…
Pathway analysis of high-throughput biological data within a Bayesian network framework
2011
Abstract Motivation: Most current approaches to high-throughput biological data (HTBD) analysis either perform individual gene/protein analysis or, gene/protein set enrichment analysis for a list of biologically relevant molecules. Bayesian Networks (BNs) capture linear and non-linear interactions, handle stochastic events accounting for noise, and focus on local interactions, which can be related to causal inference. Here, we describe for the first time an algorithm that models biological pathways as BNs and identifies pathways that best explain given HTBD by scoring fitness of each network. Results: Proposed method takes into account the connectivity and relatedness between nodes of the p…
Blind Source Separation Based on Joint Diagonalization in R: The Packages JADE and BSSasymp
2017
Blind source separation (BSS) is a well-known signal processing tool which is used to solve practical data analysis problems in various fields of science. In BSS, we assume that the observed data consists of linear mixtures of latent variables. The mixing system and the distributions of the latent variables are unknown. The aim is to find an estimate of an unmixing matrix which then transforms the observed data back to latent sources. In this paper we present the R packages JADE and BSSasymp. The package JADE offers several BSS methods which are based on joint diagonalization. Package BSSasymp contains functions for computing the asymptotic covariance matrices as well as their data-based es…
Algorithms and tools for protein-protein interaction networks clustering, with a special focus on population-based stochastic methods
2014
Abstract Motivation: Protein–protein interaction (PPI) networks are powerful models to represent the pairwise protein interactions of the organisms. Clustering PPI networks can be useful for isolating groups of interacting proteins that participate in the same biological processes or that perform together specific biological functions. Evolutionary orthologies can be inferred this way, as well as functions and properties of yet uncharacterized proteins. Results: We present an overview of the main state-of-the-art clustering methods that have been applied to PPI networks over the past decade. We distinguish five specific categories of approaches, describe and compare their main features and …
Anthropometry: An R Package for Analysis of Anthropometric Data
2017
The development of powerful new 3D scanning techniques has enabled the generation of large up-to-date anthropometric databases which provide highly valued data to improve the ergonomic design of products adapted to the user population. As a consequence, Ergonomics and Anthropometry are two increasingly quantitative fields, so advanced statistical methodologies and modern software tools are required to get the maximum benefit from anthropometric data. This paper presents a new R package, called Anthropometry, which is available on the Comprehensive R Archive Network. It brings together some statistical methodologies concerning clustering, statistical shape analysis, statistical archetypal an…
mRNAStab—a web application for mRNA stability analysis
2013
Abstract Eukaryotic gene expression is regulated both at the transcription and the mRNA degradation levels. The implementation of functional genomics methods that allow the simultaneous measurement of transcription (TR) and degradation (DR) rates for thousands of mRNAs is a huge improvement in this field. One of the best established methods for mRNA stability determination is genomic run-on (GRO). It allows the measurement of DR, TR and mRNA levels during cell dynamic responses. Here, we offer a software package that provides improved algorithms for determination of mRNA stability during dynamic GRO experiments. Availability and implementation: The program mRNAStab is freely accessible at h…
Acceleration of short and long DNA read mapping without loss of accuracy using suffix array
2014
HPG Aligner applies suffix arrays for DNA read mapping. This implementation produces a highly sensitive and extremely fast mapping of DNA reads that scales up almost linearly with read length. The approach presented here is faster (over 20 for long reads) and more sensitive (over 98% in a wide range of read lengths) than the current state-of-the-art mappers. HPG Aligner is not only an optimal alternative for current sequencers but also the only solution available to cope with longer reads and growing throughputs produced by forthcoming sequencing technologies.
Overall Objective Priors
2015
In multi-parameter models, reference priors typically depend on the parameter or quantity of interest, and it is well known that this is necessary to produce objective posterior distributions with optimal properties. There are, however, many situations where one is simultaneously interested in all the parameters of the model or, more realistically, in functions of them that include aspects such as prediction, and it would then be useful to have a single objective prior that could safely be used to produce reasonable posterior inferences for all the quantities of interest. In this paper, we consider three methods for selecting a single objective prior and study, in a variety of problems incl…