Keyword

differential expression analysis

Description: A statistical analysis method for identifying genes or other molecular features whose expression levels differ between biological conditions.

Primary topic: Gene expression and cancer classification (30%)

OpenAlex ID: keywords/differential-expression-analysis

edgeR : a Bioconductor package for differential expression analysis of digital gene expression data

2009 · Mark D. Robinson, Davis J. McCarthy, et al. · Bioinformatics · 41,239

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limma powers differential expression analyses for RNA-sequencing and microarray studies

2015 · Matthew E. Ritchie, Belinda Phipson, et al. · Nucleic Acids Research · 40,200

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HTSeq—a Python framework to work with high-throughput sequencing data

2014 · Simon Anders, Paul Theodor Pyl, et al. · Bioinformatics · 21,377

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Salmon provides fast and bias-aware quantification of transcript expression

2017 · Rob Patro, Geet Duggal, et al. · Nature Methods · 12,617

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GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses

2017 · Zefang Tang, Chenwei Li, et al. · Nucleic Acids Research · 9,828

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The National Center for Biotechnology Information

1990 · Dennis Benson, Mark Boguski, et al. · Genomics · 5,126

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data

2009 · Likun Wang, Zhixing Feng, et al. · Bioinformatics · 4,545

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Software for Computing and Annotating Genomic Ranges

2013 · Michael Lawrence, Wolfgang Huber, et al. · PLoS Computational Biology · 4,411

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The nf-core framework for community-curated bioinformatics pipelines

2020 · Philip A. Ewels, Alexander Peltzer, et al. · Nature Biotechnology · 4,063

Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences

2015 · Charlotte Soneson, Michael I. Love, et al. · F1000Research · 3,910

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Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center

2016 · Alice R. Wattam, James J. Davis, et al. · Nucleic Acids Research · 1,658

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From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline

2016 · Yunshun Chen, Aaron T. L. Lun, et al. · F1000Research · 1,301

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A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

2012 · M.-A. Dillies, A. Rau, et al. · Briefings in Bioinformatics · 1,297

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Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

2013 · Simon Anders, Davis J McCarthy, et al. · Nature Protocols · 1,146

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TISCH: a comprehensive web resource enabling interactive single-cell transcriptome visualization of tumor microenvironment

2020 · Dongqing Sun, Jin Wang, et al. · Nucleic Acids Research · 1,084

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A comparison of methods for differential expression analysis of RNA-seq data

2013 · Charlotte Soneson, Mauro Delorenzi · BMC Bioinformatics · 886

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RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics

2012 · M. Lohse, A. M. Bolger, et al. · Nucleic Acids Research · 786

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TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets

2015 · Ying Jin, Oliver H. Tam, et al. · Bioinformatics · 738

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An accurate and robust imputation method scImpute for single-cell RNA-seq data

2018 · Wei Vivian Li, Jingyi Jessica Li · Nature Communications · 700

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TCC: an R package for comparing tag count data with robust normalization strategies

2013 · Jianqiang Sun, Tomoaki Nishiyama, et al. · BMC Bioinformatics · 628

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RNA-Seq differential expression analysis: An extended review and a software tool

2017 · Juliana Costa-Silva, Douglas Domingues, et al. · PLoS ONE · 626

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Why weight? Modelling sample and observational level variability improves power in RNA-seq analyses

2015 · Ruijie Liu, Aliaksei Z. Holik, et al. · Nucleic Acids Research · 582

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New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx

2019 · Mohamed Mounir, Marta Lucchetta, et al. · PLoS Computational Biology · 534

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NetworkAnalyst - integrative approaches for protein–protein interaction network analysis and visual exploration

2014 · Jianguo Xia, Maia J. Benner, et al. · Nucleic Acids Research · 452

PyDESeq2: a python package for bulk RNA-seq differential expression analysis

2023 · Boris Muzellec, Maria Teleńczuk, et al. · Bioinformatics · 435

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Works count: 1,770

Citation count: 182,000