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ggplot2: Elegant Graphics for Data Analysis
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TLDR
This book describes ggplot2, a new data visualization package for R that uses the insights from Leland Wilkisons Grammar of Graphics to create a powerful and flexible system for creating data graphics.Abstract:
This book describes ggplot2, a new data visualization package for R that uses the insights from Leland Wilkisons Grammar of Graphics to create a powerful and flexible system for creating data graphics. With ggplot2, its easy to: produce handsome, publication-quality plots, with automatic legends created from the plot specification superpose multiple layers (points, lines, maps, tiles, box plots to name a few) from different data sources, with automatically adjusted common scales add customisable smoothers that use the powerful modelling capabilities of R, such as loess, linear models, generalised additive models and robust regression save any ggplot2 plot (or part thereof) for later modification or reuse create custom themes that capture in-house or journal style requirements, and that can easily be applied to multiple plots approach your graph from a visual perspective, thinking about how each component of the data is represented on the final plot. This book will be useful to everyone who has struggled with displaying their data in an informative and attractive way. You will need some basic knowledge of R (i.e. you should be able to get your data into R), but ggplot2 is a mini-language specifically tailored for producing graphics, and youll learn everything you need in the book. After reading this book youll be able to produce graphics customized precisely for your problems,and youll find it easy to get graphics out of your head and on to the screen or page.read more
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Journal ArticleDOI
A Large Panel of Isogenic APP and PSEN1 Mutant Human iPSC Neurons Reveals Shared Endosomal Abnormalities Mediated by APP β-CTFs, Not Aβ
Dylan Kwart,Andrew Gregg,Claudia Scheckel,Elisabeth A Murphy,Dominik Paquet,Michael Duffield,John J. Fak,Olav Olsen,Robert B. Darnell,Marc Tessier-Lavigne,Marc Tessier-Lavigne +10 more
TL;DR: Recent advances in induced pluripotent stem cell (iPSC) and CRISPR/Cas9 genome editing technologies are used to generate a panel of isogenic knockin human iPSC lines carrying APP and/or PSEN1 mutations and support mounting evidence that β-CTF may be critical in AD pathogenesis.
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Human B cell clonal expansion and convergent antibody responses to SARS-CoV-2
Sandra C. A. Nielsen,Fan Yang,Katherine J. L. Jackson,Ramona A. Hoh,Katharina Röltgen,Grace H. Jean,Bryan A. Stevens,Ji-Yeun Lee,Arjun Rustagi,Angela J. Rogers,Abigail E. Powell,Molly Hunter,Javaria Najeeb,Ana R. Otrelo-Cardoso,Kathryn E. Yost,Bence Daniel,Kari C. Nadeau,Howard Y. Chang,Howard Y. Chang,Ansuman T. Satpathy,Theodore S. Jardetzky,Peter S. Kim,Taia T. Wang,Benjamin A. Pinsky,Catherine A. Blish,Scott D. Boyd +25 more
TL;DR: It is shown that patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) who develop coronav virus disease 2019 (COVID-19) display early recruitment of B cells expressing a limited subset of IGHV genes, progressing to a highly polyclonal response of B Cells with broader I GHV gene usage and extensive class switching to IgG and IgA subclasses with limited somatic hypermutation in the initial weeks of infection.
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Experimental Effects and Individual Differences in Linear Mixed Models: Estimating the Relationship between Spatial, Object, and Attraction Effects in Visual Attention.
TL;DR: In this paper, a joint LMM analysis of experimental effects and associated subject-related variances and correlations with two frequently used alternative statistical procedures is presented, showing that slow subjects engage attention more strongly at the cued location than fast subjects.
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Caloric Restriction Reprograms the Single-Cell Transcriptional Landscape of Rattus Norvegicus Aging.
Shuai Ma,Shuhui Sun,Lingling Geng,Lingling Geng,Moshi Song,Wei Wang,Yanxia Ye,Qianzhao Ji,Zhiran Zou,Si Wang,Si Wang,Xiaojuan He,Wei Li,Concepcion Rodriguez Esteban,Xiao Long,Guoji Guo,Piu Chan,Qi Zhou,Juan Carlos Izpisua Belmonte,Weiqi Zhang,Jing Qu,Guang-Hui Liu +21 more
TL;DR: This work builds comprehensive single-cell and single-nucleus transcriptomic atlases across various rat tissues undergoing aging and CR, enhances the understanding of the robustness of CR as a geroprotective intervention, and uncovers how metabolic intervention can act upon the immune system to modify the process of aging.
Journal ArticleDOI
RWTY (R We There Yet): An R Package for Examining Convergence of Bayesian Phylogenetic Analyses.
TL;DR: RWTY as mentioned in this paper is an R package that implements established and new methods for diagnosing phylogenetic MCMC convergence in a single convenient interface, which can be used for large data sets.