ArticleRNA biology2021
3D RNA-seq: a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists.
Article in RNA biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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Who cites it
79 citing papers in PubMed, 1 synthesis or guideline pooled it, 143 citations in OpenAlex.
- RNfuzzyApp: an R shiny RNA-seq data analysis app for visualisation, differential expression analysis, time-series clustering and enrichment analysis.F1000Research · 2021Pooled it
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- SnRK2.4 and SnRK2.10 redundantly control developmental leaf senescence by sustaining ABA production and signaling.Plant physiology · 2026Article
- Genetic markers of stomatal cluster development in Begoniaceae revealed through trait analysis assisted by interactive deep-learning.Plant physiology · 2026Article
- A functionally integrated cross-tissue alternative splicing program during short-term calorie restriction.Life metabolism · 2026Article
- Alternative splicing: an underexplored layer in immune receptor regulation, systemic resistance and priming.Frontiers in plant science · 2026Article
- Transcriptomic Profiling of Orbital Fat Tissue and Ocular Surface Wash in Active Thyroid Eye Disease Requiring Urgent Orbital Decompression.Investigative ophthalmology & visual science · 2025Article
- Phosphorus starvation-induced alternative splicing landscape of rice confirms the regulatory function of Pup1 QTL.BMC plant biology · 2025Article
- The basic helix-loop-helix (bHLH) transcription factor DTT1 is part of a paired key that unlocks the tapetum transition in barley anther development.The Plant cell · 2025Article
- SON-dependent nuclear speckle rehabilitation alleviates proteinopathies.Nature communications · 2025Article
- Expression patterns of melanin-related genes are linked to crypsis and conspicuousness in a pumpkin toadlet.Molecular ecology · 2025Article
- Article
- Genome-wide and transcriptome analysis of PdWRKY transcription factors in date palm (Phoenix dactylifera) revealing insights into heat and drought stress tolerance.BMC genomics · 2025Article
- At-RS31 orchestrates hierarchical cross-regulation of splicing factors and integrates alternative splicing with TOR-ABA pathways.The New phytologist · 2025Article
- Changes in Evolutionary Developmental Control Points in the Amniote Limb May Explain Hyperphalangy.Molecular biology and evolution · 2025Article
- Mapping the molecular signature of ABA-regulated gene expression in germinating barley embryos.BMC plant biology · 2025Article
- SON-dependent nuclear speckle rehabilitation alleviates proteinopathies.bioRxiv : the preprint server for biology · 2025Article
- CLAVATA signalling shapes barley inflorescence by controlling activity and determinacy of shoot meristem and rachilla.Nature communications · 2025Article
19 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
RNA-sequencing (RNA-seq) analysis of gene expression and alternative splicing should be routine and robust but is often a bottleneck for biologists because of different and complex analysis programs and reliance on specialized bioinformatics skills. We have developed the '3D RNA-seq' App, an R shiny App and web-based pipeline for the comprehensive analysis of RNA-seq data from any organism. It represents an easy-to-use, flexible and powerful tool for analysis of both gene and transcript-level gene expression to identify differential gene/transcript expression, differential alternative splicing and differential transcript usage (3D) as well as isoform switching from RNA-seq data. 3D RNA-seq integrates state-of-the-art differential expression analysis tools and adopts best practice for RNA-seq analysis. The program is designed to be run by biologists with minimal bioinformatics experience (or by bioinformaticians) allowing lab scientists to analyse their RNA-seq data. It achieves this by operating through a user-friendly graphical interface which automates the data flow through the programs in the pipeline. The comprehensive analysis performed by 3D RNA-seq is extremely rapid and accurate, can handle complex experimental designs, allows user setting of statistical parameters, visualizes the results through graphics and tables, and generates publication quality figures such as heat-maps, expression profiles and GO enrichment plots. The utility of 3D RNA-seq is illustrated by analysis of data from a time-series of cold-treated Arabidopsis plants and from dexamethasone-treated male and female mouse cortex and hypothalamus data identifying dexamethasone-induced sex- and brain region-specific differential gene expression and alternative splicing.
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Registered trials
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.