ReviewGenome biology2016
A survey of best practices for RNA-seq data analysis.
Review in Genome biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 1,447 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
1,447 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Freely available genomic datasets for atrial fibrillation research: current resources and analytical pipeline.Frontiers in genetics · 2026Pooled it
- Guidelines to Study Transcriptome Remodeling by Proteins Using Deep Sequencing (RNA-Seq).Methods in molecular biology (Clifton, N.J.) · 2027Article
- Cortical transcriptomic dysregulation in Autism spectrum disorder: A conceptual synthesis.IBRO neuroscience reports · 2026Review
- Comparative transcriptomic and metabolomic profiling of forest tea and terrace tea in Sandu, Guizhou, China.Food chemistry. Molecular sciences · 2026Article
- Landscape transcriptomics reveals ecological constraints on fish under anthropogenic coastal change.Nature communications · 2026Article
- Long-read sequencing-based atlas of tissue-specific expression of DNM1L transcript variants.The FEBS journal · 2026Article
- Integrated Transcriptomic Analysis of Skin Pigmentation Development inInternational journal of molecular sciences · 2026Article
- Dual Modulation of Lipid Metabolism by Adzuki Bean (Foods (Basel, Switzerland) · 2026Article
- Transcriptomic and Histological Responses to Fish Meal Substitution with Soy Protein Concentrate in Formulated Feed in Totoaba (Totoaba macdonaldi) Juveniles.Marine biotechnology (New York, N.Y.) · 2026Article
- Article
- Comprehensive Bioinformatic and miRNA-Driven Analysis of the Multimeric Canonical I Kappa B Kinase (IKK) Complex in Uterine Corpus Endometrial Carcinoma (UCEC).Biomolecules · 2026Article
- Embryotoxicity of pyrethroid insecticides and their mixtures in a human induced pluripotent stem cell-based model in vitro.Archives of toxicology · 2026Article
- Mapping ovarian cellular and molecular landscape across the lifespan of women: a scoping review.Human reproduction update · 2026Article
- Long non-coding RNA triplex-dependent regulation of melanoma gene networks.NAR genomics and bioinformatics · 2026Article
- Advances in Poultry RNA-Omics Research: Technologies, RNA Information Layers, and Applications in Complex Traits.Animals : an open access journal from MDPI · 2026Review
- Mycoplasma infection drives EGFR-TKI resistance through convergent transcriptomic reprogramming in non-small cell lung cancer.iScience · 2026Article
- Increasing usable reads in RNA-seq protocols.iScience · 2026Article
- Seminal Vesicle Abnormalities and Exploratory miR-664-5p and FOXO Findings in Aged Mice Following Long-Term Butyl Benzyl Phthalate Exposure.Antioxidants (Basel, Switzerland) · 2026Article
- Effects of Fertilizer Rates on Growth ofLife (Basel, Switzerland) · 2026Article
- Integrated Analyses of mRNA and microRNA Regulatory Networks at Different Soil Moisture in Tropical EarthwormBiology · 2026Article
1,387 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
11 authors.
Funding
Abstract
RNA-sequencing (RNA-seq) has a wide variety of applications, but no single analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data analysis, including experimental design, quality control, read alignment, quantification of gene and transcript levels, visualization, differential gene expression, alternative splicing, functional analysis, gene fusion detection and eQTL mapping. We highlight the challenges associated with each step. We discuss the analysis of small RNAs and the integration of RNA-seq with other functional genomics techniques. Finally, we discuss the outlook for novel technologies that are changing the state of the art in transcriptomics.
Indexed as
Identifiers
What OpenQuestion holds
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.