ggVolcanoR: A Shiny app for customizable visualization of differential expression datasets

Kim, 2011, Identifying causal genes and dysregulated pathways in complex diseases, PLoS Comput Biol, 7, 10.1371/journal.pcbi.1001095 Schadt, 2009, Molecular networks as sensors and drivers of common human diseases, Nature, 461, 218, 10.1038/nature08454 Venkat, 2021, Drivers of Gene Expression Dysregulation in Pancreatic Cancer, Trends Cancer, 7, 594, 10.1016/j.trecan.2021.01.008 Wang, 2014, Dysregulation of gene expression as a cause of Cockayne syndrome neurological disease, Proc Natl Acad Sci U S A, 111, 14454, 10.1073/pnas.1412569111 Goncalves, 2021, IFNgamma Modulates the Immunopeptidome of Triple Negative Breast Cancer Cells by Enhancing and Diversifying Antigen Processing and Presentation, Front Immunol, 12, 10.3389/fimmu.2021.645770 Gupta, 2014, Transcriptome analysis reveals dysregulation of innate immune response genes and neuronal activity-dependent genes in autism, Nat Commun, 5, 5748, 10.1038/ncomms6748 Hecker, 2019, Blood transcriptome profiling captures dysregulated pathways and response to treatment in neuroimmunological disease, EBioMedicine, 49, 2, 10.1016/j.ebiom.2019.10.035 Lapek, 2017, Detection of dysregulated protein-association networks by high-throughput proteomics predicts cancer vulnerabilities, Nat Biotechnol, 35, 983, 10.1038/nbt.3955 Hegde, 2003, Interplay of transcriptomics and proteomics, Curr Opin Biotechnol, 14, 647, 10.1016/j.copbio.2003.10.006 Pavelka, 2008, Statistical similarities between transcriptomics and quantitative shotgun proteomics data, Mol Cell Proteomics, 7, 631, 10.1074/mcp.M700240-MCP200 Schenk, 2019, Combined transcriptome and proteome profiling reveals specific molecular brain signatures for sex, maturation and circalunar clock phase, Elife, 8, 10.7554/eLife.41556 Wang, 2019, A deep proteome and transcriptome abundance atlas of 29 healthy human tissues, Mol Syst Biol, 15, 10.15252/msb.20188503 Zhang, 2018, Transcriptomics and Targeted Proteomics Analysis to Gain Insights Into the Immune-control Mechanisms of HIV-1 Infected Elite Controllers, EBioMedicine, 27, 40, 10.1016/j.ebiom.2017.11.031 Blighe K, Rana S, Lewis M (2021), 'EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling'. Surujon, 2020, ShinyOmics: collaborative exploration of omics-data, BMC Bioinf, 21, 22, 10.1186/s12859-020-3360-x Schultheis, 2019, WIlsON: Web-based Interactive Omics VisualizatioN, Bioinformatics, 35, 1055, 10.1093/bioinformatics/bty711 Goedhart, 2020, VolcaNoseR is a web app for creating, exploring, labeling and sharing volcano plots, Sci Rep, 10, 20560, 10.1038/s41598-020-76603-3 Love, 2014, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol, 15, 550, 10.1186/s13059-014-0550-8 Harshbarger, 2017, DEIVA: a web application for interactive visual analysis of differential gene expression profiles, BMC Genomics, 18, 47, 10.1186/s12864-016-3396-5 Kallio, 2011, Chipster: user-friendly analysis software for microarray and other high-throughput data, BMC Genomics, 12, 507, 10.1186/1471-2164-12-507 Li, 2017, DEApp: an interactive web interface for differential expression analysis of next generation sequence data, Source Code Biol Med, 12, 2, 10.1186/s13029-017-0063-4 Wang, 2017, WebMeV: A Cloud Platform for Analyzing and Visualizing Cancer Genomic Data, Cancer Res, 77, e11, 10.1158/0008-5472.CAN-17-0802 Younesy, 2015, VisRseq: R-based visual framework for analysis of sequencing data, BMC Bioinf, 16, S2, 10.1186/1471-2105-16-S11-S2 Wickham H, Averick M, Bryan J, Chang W, McGowan LD, François R, et al. Welcome to the tidyverse. Journal of Open Source Software;4. Wickham, 2016 Slowikowski K, Schep A, Hughes S, Dang TK, Lukauskas S, Irisson J-O, et al. (2021), 'ggrepel: Automatically Position Non-Overlapping Text Labels with 'ggplot2''. Chang W, Cheng J, Allaire JJ, Sievert C, Schloerke B, Xie Y, et al. (2021), 'shiny: Web Application Framework for R'. Bailey E (2015), 'shinyBS: Twitter Bootstrap Components for Shiny'. Auguie, 2017 Xie Y, Cheng J, Tan X, Allaire JJ, Girlich M, Ellis GF, et al. 'DT: A Wrapper of the JavaScript Library 'DataTables''. Wickham, 2011, The Split-Apply-Combine Strategy for Data Analysis, J Stat Softw, 40, 29, 10.18637/jss.v040.i01 Wickham H, François R, Henry L, Müller K, RStudio (2021), 'dplyr: A Grammar of Data Manipulation'. Wickham, 2007, Reshaping Data with the reshape Package, J Stat Softw, 21, 20, 10.18637/jss.v021.i12 Attali D. Colourpicker: A colour picker tool for shiny and for selecting colours in plots. R package version 2017;1. Gu, 2016, Complex heatmaps reveal patterns and correlations in multidimensional genomic data, Bioinformatics, 32, 2847, 10.1093/bioinformatics/btw313 Gu, 2014, circlize implements and enhances circular visualization in R, Bioinformatics, 30, 2811, 10.1093/bioinformatics/btu393 Stelzer G, Rosen N, Plaschkes I, Zimmerman S, Twik M, Fishilevich S, et al. The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses. Curr Protoc Bioinformatics 2016;54:1 30 1-1 3. Thul, 2017, A subcellular map of the human proteome, Science, 356, 10.1126/science.aal3321 UniProt Consortium, 2021, UniProt: the universal protein knowledgebase in 2021, Nucleic Acids Res, 49, D480, 10.1093/nar/gkaa1100 Howe, 2021, Ensembl 2021, Nucleic Acids Res, 49, D884, 10.1093/nar/gkaa942 Reimand, 2007, g:Profiler–a web-based toolset for functional profiling of gene lists from large-scale experiments, Nucleic Acids Res, 35, W193, 10.1093/nar/gkm226 Willforss, 2021, OmicLoupe: facilitating biological discovery by interactive exploration of multiple omic datasets and statistical comparisons, BMC Bioinf, 22, 107, 10.1186/s12859-021-04043-5