ArticleHuman genomics2010
A survey of statistical software for analysing RNA-seq data.
Article in Human genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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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.
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Who cites it
15 citing papers in PubMed.
- Comparative Transcriptional Analysis of Long Noncoding RNAs in Oxidative Stress and Inflammation Induced by Potassium Permanganate and Lipopolysaccharide in Rat Uterine Tissues.Antioxidants (Basel, Switzerland) · 2025Article
- Plant Transcriptome Analysis with HISAT-StringTie-Ballgown and TopHat-Cufflinks Pipelines.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Host miR-129-5p reverses effects of ginsenoside Rg1 on morphine reward possibly mediated by changes inGut microbes · 2023Article
- Finite mixtures of matrix variate Poisson-log normal distributions for three-way count data.Bioinformatics (Oxford, England) · 2023Article
- Cross-platform genomic identification and clinical validation of breast cancer diagnostic biomarkers.Aging · 2021Article
- Transcriptional Profiling of Exosomes Derived fromOxidative medicine and cellular longevity · 2021Article
- Analysis of LncRNA-mRNA Co-Expression Profiles in Patients With Polycystic Ovary Syndrome: A Pilot Study.Frontiers in immunology · 2021Article
- Systematic comparison and assessment of RNA-seq procedures for gene expression quantitative analysis.Scientific reports · 2020Article
- Transcriptome analysis reveals the protection mechanism of proanthocyanidins for Saccharomyces cerevisiae during wine fermentation.Scientific reports · 2020Article
- Long noncoding RNA and mRNA profiling in cetuximab-resistant colorectal cancer cells by RNA sequencing analysis.Cancer medicine · 2019Article
- Bioinformatics challenges and perspectives when studying the effect of epigenetic modifications on alternative splicing.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2018Review
- The Epigenome of Schistosoma mansoni Provides Insight about How Cercariae Poise Transcription until Infection.PLoS neglected tropical diseases · 2015Article
- Modeling Expression Plasticity of Genes that Differentiate Drug-sensitive from Drug-resistant Cells to Chemotherapeutic Treatment.Current genomics · 2014Article
- ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions.Nature reviews. Genetics · 2012Review
- Differential gene expression in tamoxifen-resistant breast cancer cells revealed by a new analytical model of RNA-Seq data.PloS one · 2012Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-throughput RNA sequencing is rapidly emerging as a favourite method for gene expression studies. We review three software packages - edgeR, DEGseq and baySeq - from Bioconductor http://bioconductor.org for analysing RNA-sequencing data. We focus on three aspects: normalisation, statistical models and the testing employed on these methods. We also discuss the advantages and limitations of these software packages.
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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.