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The Gene Expression Omnibus (GEO) project was initiated in response to the growing demand for a public repository for high-throughput gene expression data. GEO provides a flexible and open design that facilitates submiss...

MOTIVATION: A large choice of tools exists for many standard tasks in the analysis of high-throughput sequencing (HTS) data. However, once a project deviates from standard workflows, custom scripts are needed. RESULTS: W...

When making sampling distribution inferences about the parameter of the data, θ, it is appropriate to ignore the process that causes missing data if the missing data are ‘missing at random’ and the observed data are...

Offers an applications-oriented approach to multivariate data analysis, focusing on the use of each technique, rather than its mathematical derivation. The text introduces a six-step framework for organizing and discussi...

Scanpy is a scalable toolkit for analyzing single-cell gene expression data. It includes methods for preprocessing, visualization, clustering, pseudotime and trajectory inference, differential expression testing, and sim...

In management contexts, mathematical programming is usually used to evaluate a collection of possible alternative courses of action en route to selecting one which is best. In this capacity, mathematical programming serv...

Preface.PART I: OVERVIEW AND BASIC APPROACHES.Introduction.Missing Data in Experiments.Complete-Case and Available-Case Analysis, Including Weighting Methods.Single Imputation Methods.Estimation of Imputation Uncertainty...

The Cambridge Structural Database (CSD) contains a complete record of all published organic and metal-organic small-molecule crystal structures. The database has been in operation for over 50 years and continues to be th...

The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition ...

MOTIVATION: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling ...

A software package for the analysis of X-ray absorption spectroscopy (XAS) data is presented. This package is based on the IFEFFIT library of numerical and XAS algorithms and is written in the Perl programming language u...

Machine learning addresses the question of how to build computers that improve automatically through experience. It is one of today's most rapidly growing technical fields, lying at the intersection of computer science a...

Amazon's Mechanical Turk (MTurk) is a relatively new website that contains the major elements required to conduct research: an integrated participant compensation system; a large participant pool; and a streamlined proce...

BACKGROUND: A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de fa...

In this article, the authors describe how they used a hybrid process of inductive and deductive thematic analysis to interpret raw data in a doctoral study on the role of performance feedback in the self-assessment of nu...

Tremendous amount of RNA sequencing data have been produced by large consortium projects such as TCGA and GTEx, creating new opportunities for data mining and deeper understanding of gene functions. While certain existin...

Guidelines for determining nonprobabilistic sample sizes are virtually nonexistent. Purposive samples are the most commonly used form of nonprobabilistic sampling, and their size typically relies on the concept of “sat...

The cBioPortal for Cancer Genomics (http://cbioportal.org) provides a Web resource for exploring, visualizing, and analyzing multidimensional cancer genomics data. The portal reduces molecular profiling data from cancer ...

AIM: The aim of this paper is to distinguish the integrative review method from other review methods and to propose methodological strategies specific to the integrative review method to enhance the rigour of the process...

The R package mice imputes incomplete multivariate data by chained equations. The software mice 1.0 appeared in the year 2000 as an S-PLUS library, and in 2001 as an R package. mice 1.0 introduced predictor selection, pa...

A measure is presented which indicates the similarity of clusters which are assumed to have a data density which is a decreasing function of distance from a vector characteristic of the cluster. The measure can be used t...

Deep learning has revolutionized many machine learning tasks in recent years, ranging from image classification and video processing to speech recognition and natural language understanding. The data in these tasks are t...

The NCEP and NCAR are cooperating in a project (denoted “reanalysis”) to produce a 40-year record of global analyses of atmospheric fields in support of the needs of the research and climate monitoring communities. T...

We developed interpolated climate surfaces for global land areas (excluding Antarctica) at a spatial resolution of 30 arc s (often referred to as 1-km spatial resolution). The climate elements considered were monthly pre...