Extends the functionality of other plotting packages (notably 'ggplot2')
    to help facilitate the plotting of data over long time intervals, including,
    but not limited to, geological, evolutionary, and ecological data. The
    primary goal of 'deeptime' is to enable users to add highly customizable
    timescales to their visualizations. Other functions are also included to
    assist with other areas of deep time visualization.

Allows for the specification of deep conditional transformation 
    models (DCTMs) and ordinal neural network transformation models, as 
    described in Baumann et al (2021) <doi:10.1007/978-3-030-86523-8_1> and 
    Kook et al (2022) <doi:10.1016/j.patcog.2021.108263>. Extensions such as
    autoregressive DCTMs (Ruegamer et al, 2022, <doi:10.48550/arXiv.2110.08248>)
    and transformation ensembles (Kook et al, 2022, <doi:10.48550/arXiv.2205.12729>)
    are implemented.

Abstract of Manuscript. Differential gene expression analysis using RNA sequencing (RNA-seq) data is a standard approach for making biological discoveries. Ongoing large-scale efforts to process and normalize publicly available gene expression data enable rapid and systematic reanalysis. While several powerful tools systematically process RNA-seq data, enabling their reanalysis, few resources systematically recompute differentially expressed genes (DEGs) generated from individual studies. We developed a robust differential expression analysis pipeline to recompute 3162 human DEG lists from The Cancer Genome Atlas, Genotype-Tissue Expression Consortium, and 142 studies within the Sequence Read Archive. After measuring the accuracy of the recomputed DEG lists, we built the Differential Expression Enrichment Tool (DEET), which enables users to interact with the recomputed DEG lists. DEET, available through CRAN and RShiny, systematically queries which of the recomputed DEG lists share similar genes, pathways, and TF targets to their own gene lists. DEET identifies relevant studies based on shared results with the user’s gene lists, aiding in hypothesis generation and data-driven literature review. Sokolowski, Dustin J., et al. "Differential Expression Enrichment Tool (DEET): an interactive atlas of human differential gene expression." Nucleic Acids Research Genomics and Bioinformatics (2023).