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Programming Graphical User Interfaces in R
Focusing on graphic user interfaces (GUIs) within the R language, this book shows programmers and users how to develop their own GUIs, enabling them to interface with other languages. The text opens the possibilities of R's huge and growing set of statistical methods. The authors cover four different packages for writing GUIs: gWidgets, RGtk2, Qt, and Tcl Tk. Supported by a package in CRAN that contains all of the code along with additional examples, the text is filled with numerous examples ranging from the very simple to detailed illustrations of how to code actual interfaces.
eBook
The triumphs and limitations of computational methods for scRNA-seq
The rapid progress of protocols for sequencing single-cell transcriptomes over the past decade has been accompanied by equally impressive advances in the computational methods for analysis of such data. As capacity and accuracy of the experimental techniques grew, the emerging algorithm developments revealed increasingly complex facets of the underlying biology, from cell type composition to gene regulation to developmental dynamics. At the same time, rapid growth has forced continuous reevaluation of the underlying statistical models, experimental aims, and sheer volumes of data processing that are handled by these computational tools. Here, I review key computational steps of single-cell RNA sequencing (scRNA-seq) analysis, examine assumptions made by different approaches, and highlight successes, remaining ambiguities, and limitations that are important to keep in mind as scRNA-seq becomes a mainstream technique for studying biology.This review provides an overview of recent computational developments in scRNA-seq analysis and highlights packages and tools applied in executing these analyses.
Journal Article
metaX: a flexible and comprehensive software for processing metabolomics data
Background
Non-targeted metabolomics based on mass spectrometry enables high-throughput profiling of the metabolites in a biological sample. The large amount of data generated from mass spectrometry requires intensive computational processing for annotation of mass spectra and identification of metabolites. Computational analysis tools that are fully integrated with multiple functions and are easily operated by users who lack extensive knowledge in programing are needed in this research field.
Results
We herein developed an R package, metaX, that is capable of end-to-end metabolomics data analysis through a set of interchangeable modules. Specifically, metaX provides several functions, such as peak picking and annotation, data quality assessment, missing value imputation, data normalization, univariate and multivariate statistics, power analysis and sample size estimation, receiver operating characteristic analysis, biomarker selection, pathway annotation, correlation network analysis, and metabolite identification. In addition, metaX offers a web-based interface (
http://metax.genomics.cn
) for data quality assessment and normalization method evaluation, and it generates an HTML-based report with a visualized interface. The metaX utilities were demonstrated with a published metabolomics dataset on a large scale. The software is available for operation as either a web-based graphical user interface (GUI) or in the form of command line functions. The package and the example reports are available at
http://metax.genomics.cn/
.
Conclusions
The pipeline of metaX is platform-independent and is easy to use for analysis of metabolomics data generated from mass spectrometry.
Journal Article
Understanding The New Statistics
This is the first book to introduce the new statistics - effect sizes, confidence intervals, and meta-analysis - in an accessible way. It is chock full of practical examples and tips on how to analyze and report research results using these techniques. The book is invaluable to readers interested in meeting the new APA Publication Manual guidelines by adopting the new statistics - which are more informative than null hypothesis significance testing, and becoming widely used in many disciplines.
Accompanying the book is the Exploratory Software for Confidence Intervals (ESCI) package, free software that runs under Excel and is accessible at www.thenewstatistics.com. The book's exercises use ESCI's simulations, which are highly visual and interactive, to engage users and encourage exploration. Working with the simulations strengthens understanding of key statistical ideas. There are also many examples, and detailed guidance to show readers how to analyze their own data using the new statistics, and practical strategies for interpreting the results. A particular strength of the book is its explanation of meta-analysis, using simple diagrams and examples. Understanding meta-analysis is increasingly important, even at undergraduate levels, because medicine, psychology and many other disciplines now use meta-analysis to assemble the evidence needed for evidence-based practice.
The book's pedagogical program, built on cognitive science principles, reinforces learning:
Boxes provide \"evidence-based\" advice on the most effective statistical techniques.
Numerous examples reinforce learning, and show that many disciplines are using the new statistics.
Graphs are tied in with ESCI to make important concepts vividly clear and memorable.
Opening overviews and end of chapter take-home messages summarize key points.
Exercises encourage exploration, deep understanding, and practical app
eBook
Graph convolutional networks: a comprehensive review
Graphs naturally appear in numerous application domains, ranging from social analysis, bioinformatics to computer vision. The unique capability of graphs enables capturing the structural relations among data, and thus allows to harvest more insights compared to analyzing data in isolation. However, it is often very challenging to solve the learning problems on graphs, because (1) many types of data are not originally structured as graphs, such as images and text data, and (2) for graph-structured data, the underlying connectivity patterns are often complex and diverse. On the other hand, the representation learning has achieved great successes in many areas. Thereby, a potential solution is to learn the representation of graphs in a low-dimensional Euclidean space, such that the graph properties can be preserved. Although tremendous efforts have been made to address the graph representation learning problem, many of them still suffer from their shallow learning mechanisms. Deep learning models on graphs (e.g., graph neural networks) have recently emerged in machine learning and other related areas, and demonstrated the superior performance in various problems. In this survey, despite numerous types of graph neural networks, we conduct a comprehensive review specifically on the emerging field of graph convolutional networks, which is one of the most prominent graph deep learning models. First, we group the existing graph convolutional network models into two categories based on the types of convolutions and highlight some graph convolutional network models in details. Then, we categorize different graph convolutional networks according to the areas of their applications. Finally, we present several open challenges in this area and discuss potential directions for future research.
Journal Article
Joint estimation of multiple graphical models
Gaussian graphical models explore dependence relationships between random variables, through the estimation of the corresponding inverse covariance matrices. In this paper we develop an estimator for such models appropriate for data from several graphical models that share the same variables and some of the dependence structure. In this setting, estimating a single graphical model would mask the underlying heterogeneity, while estimating separate models for each category does not take advantage of the common structure. We propose a method that jointly estimates the graphical models corresponding to the different categories present in the data, aiming to preserve the common structure, while allowing for differences between the categories. This is achieved through a hierarchical penalty that targets the removal of common zeros in the inverse covariance matrices across categories. We establish the asymptotic consistency and sparsity of the proposed estimator in the high-dimensional case, and illustrate its performance on a number of simulated networks. An application to learning semantic connections between terms from webpages collected from computer science departments is included.
Journal Article
Drug-disease networks and drug repurposing
Repurposing existing drugs to treat new diseases is a cost-effective alternative to de novo drug development, but there are millions of potential drug-disease combinations to be considered with only a small fraction being viable. In silico predictions of drug-disease associations can be invaluable for reducing the size of the search space. In this work we present a novel network of drugs and the diseases they treat, compiled using a combination of existing textual and machine-readable databases, natural-language processing tools, and hand curation, and analyze it using network-based link prediction methods to identify potential drug-disease combinations. We measure the efficacy of these methods using cross-validation tests and find that several methods, particularly those based on graph embedding and network model fitting, achieve impressive prediction performance, significantly better than previous approaches, with area under the ROC curve above 0.95 and average precision almost a thousand times better than chance.
Journal Article
Integrating multiple spatial transcriptomics data using community-enhanced graph contrastive learning
Due to the rapid development of spatial sequencing technologies, large amounts of spatial transcriptomic datasets have been generated across various technological platforms or different biological conditions (e.g., control vs. treatment). Spatial transcriptomics data coming from different platforms usually has different resolutions. Moreover, current methods do not consider the heterogeneity of spatial structures within and across slices when modeling spatial transcriptomics data with graph-based methods. In this study, we propose a community-enhanced graph contrastive learning-based method named Tacos to integrate multiple spatial transcriptomics data. We applied Tacos to several real datasets coming from different platforms under different scenarios. Systematic benchmark analyses demonstrate Tacos’s superior performance in integrating different slices. Furthermore, Tacos can accurately denoise the spatially resolved transcriptomics data.
Journal Article
MultiModalGraphics: an R package for graphical integration of multi-omics datasets
Multimodal visualizations are essential for identifying and interpreting complex relationships in diverse, high-dimensional biological datasets. However, existing visualization tools often lack native capabilities for embedding explicit statistical and computational annotations, hindering effective quantitative interpretation. We introduce MultiModalGraphics, an R package designed specifically for creating annotated scatterplots and heatmaps of multi-omics and high-dimensional biological data. The package allows seamless embedding of statistical summaries such as fold-changes,
p
-values, q-values, and standard deviations, facilitating direct quantitative comparisons. MultiModalGraphics interoperates with Bioconductor packages including MultiAssayExperiment, limma, voom, and iClusterPlus, streamlining workflows from data preprocessing and differential expression analysis to visualization. Case studies on three distinct real-world multimodal datasets illustrate its practical utility. Source code, documentation, and example datasets are available via GitHub (
https://github.com/famanalytics0/MultiModalGraphics
) and under review for inclusion into Bioconductor.
Journal Article