ArticleBMC bioinformatics2018
Trendy: segmented regression analysis of expression dynamics in high-throughput ordered profiling experiments.
Article in BMC bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
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- Multimodal bioinformatic analyses of genome-scale expression beyond gene-centric differential expression.Briefings in bioinformatics · 2026Review
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- Time-course characterization of whole-transcriptome dynamics of HepG2/C3A spheroids and its toxicological implications.Toxicology letters · 2024Article
- Integrated Blood Transcriptome and Multi-Tissue Trace Mineral Analyses of Healthy Stocker Cattle Fed Complexed or Inorganic Trace Mineral Supplement.Animals : an open access journal from MDPI · 2024Article
- Genome-wide analysis of transcription-coupled repair reveals novel transcription events in Caenorhabditis elegans.PLoS genetics · 2024Article
- Single-cell profiling reveals transcriptome dynamics during bovine oocyte growth.BMC genomics · 2024Article
- Genome-wide analysis of transcription-coupled repair reveals novel transcription events inbioRxiv : the preprint server for biology · 2024Article
- The GRN concept as a guide for evolutionary developmental biology.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2023Article
- Belayer: Modeling discrete and continuous spatial variation in gene expression from spatially resolved transcriptomics.Cell systems · 2022Article
- Single-cell generalized trend model (scGTM): a flexible and interpretable model of gene expression trend along cell pseudotime.Bioinformatics (Oxford, England) · 2022Article
- Time Series Transcriptome Analysis inFrontiers in plant science · 2022Article
- A Brain Region-Specific Expression Profile for Genes Within Large Introgression Deserts and Under Positive Selection inFrontiers in cell and developmental biology · 2022Article
- TimesVector-Web: A Web Service for Analysing Time Course Transcriptome Data with Multiple Conditions.Genes · 2021Article
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- Interspecies chimeric conditions affect the developmental rate of human pluripotent stem cells.PLoS computational biology · 2021Article
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Authors and funding
7 authors.
Funding
Abstract
backgroundHigh-throughput expression profiling experiments with ordered conditions (e.g. time-course or spatial-course) are becoming more common for studying detailed differentiation processes or spatial patterns. Identifying dynamic changes at both the individual gene and whole transcriptome level can provide important insights about genes, pathways, and critical time points.
resultsWe present an R package, Trendy, which utilizes segmented regression models to simultaneously characterize each gene's expression pattern and summarize overall dynamic activity in ordered condition experiments. For each gene, Trendy finds the optimal segmented regression model and provides the location and direction of dynamic changes in expression. We demonstrate the utility of Trendy to provide biologically relevant results on both microarray and RNA-sequencing (RNA-seq) datasets.
conclusionsTrendy is a flexible R package which characterizes gene-specific expression patterns and summarizes changes of global dynamics over ordered conditions. Trendy is freely available on Bioconductor with a full vignette at https://bioconductor.org/packages/release/bioc/html/Trendy.html .
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.