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Abstract

High-throughput sequencing techniques are increasingly affordable and produce massive amounts of data. Together with other high-throughput technologies, such as microarrays, there are an enormous amount of resources in databases. The collection of these valuable data has been routine for more than a decade. Despite different technologies, many experiments share the same goal. For instance, the aims of RNA-seq studies often coincide with those of differential gene expression experiments based on microarrays. As such, it would be logical to utilize all available data. However, there is a lack of biostatistical tools for the integration of results obtained from different technologies. Although diverse technological platforms produce different raw data, one commonality for experiments with the same goal is that all the outcomes can be transformed into a platform-independent data format – rankings – for the same set of items. Here we present the R package TopKLists, which allows for statistical inference on the lengths of informative (top-k) partial lists, for stochastic aggregation of full or partial lists, and for graphical exploration of the input and consolidated output. A graphical user interface has also been implemented for providing access to the underlying algorithms. To illustrate the applicability and usefulness of the package, we integrated microRNA data of non-small cell lung cancer across different measurement techniques and draw conclusions. The package can be obtained from CRAN under a LGPL-3 license.

Abstract

In modern software development processes, software effort estimation plays a crucial role. The success or failure of projects depends greatly on the accuracy of effort estimation and schedule results. Many studies focused on proposing novel models to enhance the accuracy of predicted results; however, the question of accurate estimation of effort has been a challenging issue with regards to researchers and practitioners, especially when it comes to projects using agile methodologies. This study aims at introducing a novel formula based on team velocity and story point factors. The parameters of this formula are then optimized by employing swarm optimization algorithms. We also propose an improved algorithm combining the advantages of the artificial bee colony and particle swarm optimization algorithms. The experimental results indicated that our approaches outperformed methods in other studies in terms of the accuracy of predicted results.

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