Ggrepel

Manufactured by Posit

Ggrepel is a geospatial data visualization library for the R programming language. It provides a set of functions for adding repulsive labels to plots, ensuring that labels do not overlap with each other or with other elements of the plot.

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Lab products found in correlation

Ggplot2, by Posit (2 mentions) Tidyverse, by Posit (1 mentions) Dplyr, by Posit (1 mentions) Jasp software, by JASP Stats (1 mentions) Version 10, by FlowJo (1 mentions)

3 protocols using ggrepel

Statistical Analysis of Omics Data

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Data were analysed using RStudio (RRID:SCR_000432), ggplot2 (RRID:SCR_014601), dplyr (RRID:SCR_016708), tidyverse (RRID:SCR_019186), ggrepel (RRID:SCR_017393), openxlsx (RRID:SCR_019185), ggthemes, ggsignif, gridExtra and Origin (RRID:SCR_014212) software. All datasets were tested for normality using the Shapiro–Wilkinson test. When a normal distribution was confirmed, a One-Way ANOVA test with a post hoc Tukey's HSD test was used for statistical comparison between multiple groups. For datasets that did not show normality, a Kruskal–Wallis test with a post hoc Dunn's test was applied. The asterisks in the figures correspond to the following p-values: *p < 0.05, **p < 0.01 and ***p < 0.001. Experiments were performed as biological triplicates on different clones and data with error bars are represented as mean ± standard deviation .

Valenti M., Molina M, & Cid V.J. (2023). Human gasdermin D and MLKL disrupt mitochondria, endocytic traffic and TORC1 signalling in budding yeast. Open Biology, 13(5), 220366.

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Multivariate Analysis of Retinal Cell Types

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A minimum of three biological replicates was used across the study. Statistical tests were used as reported in each figure. Two-tailed student t-test for independent samples was performed in Microsoft Excel. One-way ANOVAs with a post hoc Tukey test for each timepoint using pan-RPC marker (VSX2/LHX2/PAX6) as an independent variable were calculated using the JASP software (JASP Team 2017, Version 0.8.1.2). Data run through t-test and ANOVA was verified for normal distribution using a Shapiro-Wilk test. If not normally distributed, Mann-Whitney test or Kruskall-Wallis with Dunn’s posthoc (Pohlert, 2014) test was performed using R 3.3.0. Kolmogorov-Smirnov tests were performed using R 3.3.0. RNAseq dotplots and EdU count scatterplots were created using R 3.3.0 (R Core Team, 2016 ) and RStudio 1.0.136 (RStudio Team, 2016 ) using the ggplot2 (Wickham, 2009 ) and ggrepel (Slowikowski, 2016 ) package. FACS plots were produced in FlowJo Version 10.2.

Buenaventura D.F., Tegla M.G, & Emerson M.M. (2018). Fate-restricted retinal progenitor cells adopt a molecular profile and spatial position distinct from multipotent progenitor cells. Developmental biology, 443(1), 35-49.

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RNA-seq Analysis of A. baumannii

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RNA-seq analysis was performed at the Australian Genome Research Facility. The cDNA library was prepared and assessed as described previously (19 (link)). An average of 30 million reads per sample were generated, then trimmed using trimmomatic (v0.36), and mapped to the reference genome (A. baumannii MS14413 accession number NZ_CP054302) using bowtie2 (v2.3.4.2) with default parameters (–local –very-sensitive-local). Read counts were determined using featureCounts (Rsubread v1.28.1), and differential gene expression was analyzed with edgeR (v3.20.9) and limma-voom (v3.34.9) with the counts per minute (cpm) threshold set at 2.0. Figures were generated using ggplot2 (v3.3.0) and ggrepel (v0.8.2) packages in Rstudio (61 ).

De Oliveira D.M., Forde B.M., Phan M.D., Steiner B., Zhang B., Zuegg J., El-deeb I.M., Li G., Keller N., Brouwer S., Harbison-Price N., Cork A.J., Bauer M.J., Alquethamy S.F., Beatson S.A., Roberts J.A., Paterson D.L., McEwan A.G., Blaskovich M.A., Schembri M.A., McDevitt C.A., von Itzstein M, & Walker M.J. (2022). Rescuing Tetracycline Class Antibiotics for the Treatment of Multidrug-Resistant Acinetobacter baumannii Pulmonary Infection. mBio, 13(1), e03517-21.

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