Search

Advances in spatially-resolved transcriptomics (SRT) technologies have propelled the development of new computational analysis methods to unlock biological insights. As the cost of generating these data decreases, these technologies provide an exciting opportunity to create large-scale atlases that integrate SRT data across multiple tissues, individuals, species, or phenotypes to perform population-level analyses. Here, we describe unique challenges of varying spatial resolutions in SRT data, as well as highlight the opportunities for standardized preprocessing methods along with computational algorithms amenable to atlas-scale datasets leading to improved sensitivity and reproducibility in the future., Comment: 16 pages, 2 figures

A challenge that data analysts face is building a data analysis that is useful for a given consumer. Previously, we defined a set of principles for describing data analyses that can be used to create a data analysis and to characterize the variation between analyses. Here, we introduce a concept that we call the alignment of a data analysis between the data analyst and a consumer. We define a successfully aligned data analysis as the matching of principles between the analyst and the consumer for whom the analysis is developed. In this paper, we propose a statistical model for evaluating the alignment of a data analysis and describe some of its properties. We argue that this framework provides a language for characterizing alignment and can be used as a guide for practicing data scientists and students in data science courses for how to build better data analyses.

In 1977 John Tukey described how in exploratory data analysis, data analysts use tools, such as data visualizations, to separate their expectations from what they observe. In contrast to statistical theory, an underappreciated aspect of data analysis is that a data analyst must make decisions by comparing the observed data or output from a statistical tool to what the analyst previously expected from the data. However, there is little formal guidance for how to make these data analytic decisions as statistical theory generally omits a discussion of who is using these statistical methods. In this paper, we propose a model for the iterative process of data analysis based on the analyst's expectations, using what we refer to as expected and anomaly probabilistic outcome sets, and the concept of statistical information gain. Here, we extend the basic idea of comparing an analyst's expectations to what is observed in a data visualization to more general analytic situations. Our model posits that the analyst's goal is to increase the amount of information the analyst has relative to what the analyst already knows, through successive analytic iterations. We introduce two criteria--expected information gain and anomaly information gain--to provide guidance about analytic decision-making and ultimately to improve the practice of data analysis. Finally, we show how our framework can be used to characterize common situations in practical data analysis., Comment: 30 pages

Deconvolution of cell mixtures in "bulk" transcriptomic samples from homogenate human tissue is important for understanding the pathologies of diseases. However, several experimental and computational challenges remain in developing and implementing transcriptomics-based deconvolution approaches, especially those using a single cell/nuclei RNA-seq reference atlas, which are becoming rapidly available across many tissues. Notably, deconvolution algorithms are frequently developed using samples from tissues with similar cell sizes. However, brain tissue or immune cell populations have cell types with substantially different cell sizes, total mRNA expression, and transcriptional activity. When existing deconvolution approaches are applied to these tissues, these systematic differences in cell sizes and transcriptomic activity confound accurate cell proportion estimates and instead may quantify total mRNA content. Furthermore, there is a lack of standard reference atlases and computational approaches to facilitate integrative analyses, including not only bulk and single cell/nuclei RNA-seq data, but also new data modalities from spatial -omic or imaging approaches. New multi-assay datasets need to be collected with orthogonal data types generated from the same tissue block and the same individual, to serve as a "gold standard" for evaluating new and existing deconvolution methods. Below, we discuss these key challenges and how they can be addressed with the acquisition of new datasets and approaches to analysis., Comment: 28 pages; 4 figures

With unprecedented and growing interest in data science education, there are limited educator materials that provide meaningful opportunities for learners to practice statistical thinking, as defined by Wild and Pfannkuch (1999), with messy data addressing real-world challenges. As a solution, Nolan and Speed (1999) advocated for bringing applications to the forefront in undergraduate statistics curriculum with the use of in-depth case studies to encourage and develop statistical thinking in the classroom. Limitations to this approach include the significant time investment required to develop a case study -- namely, to select a motivating question and to create an illustrative data analysis -- and the domain expertise needed. As a result, case studies based on realistic challenges, not toy examples, are scarce. To address this, we developed the Open Case Studies (https://www.opencasestudies.org) project, which offers a new statistical and data science education case study model. This educational resource provides self-contained, multimodal, peer-reviewed, and open-source guides (or case studies) from real-world examples for active experiences of complete data analyses. We developed an educator's guide describing how to most effectively use the case studies, how to modify and adapt components of the case studies in the classroom, and how to contribute new case studies. (https://www.opencasestudies.org/OCS_Guide)., Comment: 16 pages in main text, 3 figures, and 2 tables; 9 page in supplement

The data science revolution has led to an increased interest in the practice of data analysis. While much has been written about statistical thinking, a complementary form of thinking that appears in the practice of data analysis is design thinking -- the problem-solving process to understand the people for whom a product is being designed. For a given problem, there can be significant or subtle differences in how a data analyst (or producer of a data analysis) constructs, creates, or designs a data analysis, including differences in the choice of methods, tooling, and workflow. These choices can affect the data analysis products themselves and the experience of the consumer of the data analysis. Therefore, the role of a producer can be thought of as designing the data analysis with a set of design principles. Here, we introduce design principles for data analysis and describe how they can be mapped to data analyses in a quantitative, objective and informative manner. We also provide empirical evidence of variation of principles within and between both producers and consumers of data analyses. Our work leads to two insights: it suggests a formal mechanism to describe data analyses based on the design principles for data analysis, and it provides a framework to teach students how to build data analyses using formal design principles., Comment: arXiv admin note: text overlap with arXiv:1903.07639

Rapid advances in computing technology over the past few decades have spurred two extraordinary phenomena in science: large-scale and high-throughput data collection coupled with the creation and implementation of complex statistical algorithms for data analysis. Together, these two phenomena have brought about tremendous advances in scientific discovery but have also raised two serious concerns, one relatively new and one quite familiar. The complexity of modern data analyses raises questions about the reproducibility of the analyses, meaning the ability of independent analysts to re-create the results claimed by the original authors using the original data and analysis techniques. While seemingly a straightforward concept, reproducibility of analyses is typically thwarted by the lack of availability of the data and computer code that were used in the analyses. A much more general concern is the replicability of scientific findings, which concerns the frequency with which scientific claims are confirmed by completely independent investigations. While the concepts of reproduciblity and replicability are related, it is worth noting that they are focused on quite different goals and address different aspects of scientific progress. In this review, we will discuss the origins of reproducible research, characterize the current status of reproduciblity in public health research, and connect reproduciblity to current concerns about replicability of scientific findings. Finally, we describe a path forward for improving both the reproducibility and replicability of public health research in the future.

A fundamental problem in the practice and teaching of data science is how to evaluate the quality of a given data analysis, which is different than the evaluation of the science or question underlying the data analysis. Previously, we defined a set of principles for describing data analyses that can be used to create a data analysis and to characterize the variation between data analyses. Here, we introduce a metric of quality evaluation that we call the success of a data analysis, which is different than other potential metrics such as completeness, validity, or honesty. We define a successful data analysis as the matching of principles between the analyst and the audience on which the analysis is developed. In this paper, we propose a statistical model and general framework for evaluating the success of a data analysis. We argue that this framework can be used as a guide for practicing data scientists and students in data science courses for how to build a successful data analysis., Comment: 16 pages

The data revolution has led to an increased interest in the practice of data analysis. For a given problem, there can be significant or subtle differences in how a data analyst constructs or creates a data analysis, including differences in the choice of methods, tooling, and workflow. In addition, data analysts can prioritize (or not) certain objective characteristics in a data analysis, leading to differences in the quality or experience of the data analysis, such as an analysis that is more or less reproducible or an analysis that is more or less exhaustive. However, data analysts currently lack a formal mechanism to compare and contrast what makes analyses different from each other. To address this problem, we introduce a vocabulary to describe and characterize variation between data analyses. We denote this vocabulary as the elements and principles of data analysis, and we use them to describe the fundamental concepts for the practice and teaching of creating a data analysis. This leads to two insights: it suggests a formal mechanism to evaluate data analyses based on objective characteristics, and it provides a framework to teach students how to build data analyses., Comment: 14 pages, 7 figures, 1 table

Demand for data science education is surging and traditional courses offered by statistics departments are not meeting the needs of those seeking training. This has led to a number of opinion pieces advocating for an update to the Statistics curriculum. The unifying recommendation is computing should play a more prominent role. We strongly agree with this recommendation, but advocate the main priority is to bring applications to the forefront as proposed by Nolan and Speed (1999). We also argue that the individuals tasked with developing data science courses should not only have statistical training, but also have experience analyzing data with the main objective of solving real-world problems. Here, we share a set of general principles and offer a detailed guide derived from our successful experience developing and teaching a graduate-level, introductory data science course centered entirely on case studies. We argue for the importance of statistical thinking, as defined by Wild and Pfannkuck (1999) and describe how our approach teaches students three key skills needed to succeed in data science, which we refer to as creating, connecting, and computing. This guide can also be used for statisticians wanting to gain more practical knowledge about data science before embarking on teaching an introductory course., Comment: 2 tables, 3 figures, 2 supplemental figures