Comparison of software packages for detecting differential expression in RNA-seq studies

Cited by (424)

Items 301–400 of 424

1. Controlling for confounding effects in single cell RNA sequencing studies using both control and target genes
   Mengjie Chen, Xiang Zhou · 2016 · bioRxiv (Cold Spring Harbor Laboratory)
2. Effects of technical noise on bulk RNA-seq differential gene expression inference
   Dylan Sheerin, Daniel O’Connor, Andrew John Pollard, Irina I Mohorianu · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
3. Systematic benchmarking of bulk and single-cell RNA-seq statistical methods to assess differential expression of circular RNAs
   Alessia Buratin, Stefania Bortoluzzi, Enrico Gaffo · 2022 · Research Square
4. Critical Differential Expression Assessment for Individual Bulk RNA-Seq Projects
   Charles Warden, Xiwei Wu · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
5. RNA Solutions: Synthesizing Information to Support Transcriptomics (RNASSIST)
   Yi-Pei Chen, Laura B. Ferguson, Nihal A. Salem, George Zheng, Roy Dayne Mayfield, Mohammed Eslami · 2021 · Bioinformatics
6. A DECISION TREE-BASED CLASSIFIER COMPARES THREE DATA ANALYSIS METHODS FOR THE IDENTIFICATION OF MIRNAS ASSOCIATED WITH EARLY-STAGE LUNG CANCER
   Bethina da Rocha Camargo, Vanessa G. P. Souza, Rainer Marco López Lapa, Patrícia P. Reis, Rogério Antônio de Oliveira · 2023 · Revista Foco
7. CONFIDENCE: A Web App for Cross-Platform Differential Gene Expression Analysis, Gene Scoring, and Enrichment Analysis
   Abhishek Shastry, Benjamin Ott, Tanvi Nandani, Alex Paterson, Matt Simpson, Kimberly J. Dunham‐Snary, Charles C.T. Hindmarch · 2024 · Free Radical Biology and Medicine
8. Computational Analysis of RNA-Seq Data from Airway Epithelial Cells for Studying Lung Disease
   Nathan D. Jackson, Lando Ringel, Max A. Seibold · 2018 · Methods in molecular biology
9. Unbiased bioinformatics analysis of microRNA transcriptomics datasets and network theoretic target prediction
   Bence Ágg, Péter Ferdinandy · 2021 · Elsevier eBooks
10. Compositional Analysis of Microbiome Data
    Yinglin Xia, Jun Sun · 2023 · Springer eBooks
11. A Workflow Guide to RNA-Seq Analysis of Chaperone Function and Beyond
    Kristina M. Holton, Richard M. Giadone, Benjamin J. Lang, Stuart K. Calderwood · 2023 · Methods in molecular biology
12. Metabolic differentiation of brushtail possum populations resistant and susceptible to plant toxins revealed via differential gene expression
    David Carmelet‐Rescan, Mary Morgan‐Richards, Steven A. Trewick · 2024 · Journal of Comparative Physiology B
13. Identification of Genomic Instability-Associated LncRNAs as Potential Therapeutic Targets in Lung Adenocarcinoma
    Vanessa G. P. Souza, Katya Benard, Greg L. Stewart, Katey S.S. Enfield, Wan L. Lam · 2025 · Cancers
14. AIDE: annotation-assisted isoform discovery with high precision
    Shan Li, Shan Li, Xin Tong, Ling Deng, Hubing Shi, Wei Vivian Li · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
15. RNA-Seq Analysis: Methods, Applications and Challenges
    Autori vari, Geraci, F., Saha, I., Bianchini, M. · 2020 · Frontiers research topics
16. Transcriptomics to Metabolomics
    Ankush Bansal, Pulkit Anupam Srivastava · 2019 · IGI Global eBooks
17. Transcriptional response to West Nile virus infection in the zebra finch (Taeniopygia guttata), a songbird model for immune function: Data
    Hofmeister, Erik K, Christopher N. Balakrishnan, Daniel Newhouse · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
18. Lost in Transition - Genetic, Transcriptomic and Breeding Aspects of Metabolic Robustness in Dairy Cows
    Ngoc-Thuy Ha · 2016
19. Análise do transcritoma do mexilhão marrom (Perna perna) sob contaminação por antraceno
    Jhonatas Sirino Monteiro · 2017
20. Comprehensive Visualization of High-Dimensional Single-Cell Data With Diffusion-Based Manifold Approximation and Projection (dbMAP)
    Davi Sidarta-Oliveira, Licio Augusto Velloso · 2020 · SSRN Electronic Journal
21. Class Discovery, Comparison, and Prediction Methods for RNA-Seq Data
    Ahu Cephe, Necla Koçhan, Gözde Ertürk Zararsız, Vahap Eldem, Gökmen Zararsız · 2023 · IGI Global eBooks
22. PRRGO: A Tool for Visualizing and Mapping Globally Expressed Genes in Public Gene Expression Omnibus RNA-Sequencing Studies to PageRank-scored Gene Ontology Terms
    Luis E. Solano, Nicholas D’Sa, Nikolas Nikolaidis · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
23. Progression of RNA-sequencing to single-cell applications
    Daniel Ramsköld · 2014 · Figshare
24. Analysis of RNA-seq data from the interaction of Coffea spp. - Colletotrichum kahawae
    Joana Fino · 2014 · Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT)
25. Estudos sobre a organização genômica, evolução e expressão de microRNAs
    Gustavo S. França · 2016 · Digital Library of Theses and Dissertations (Universidade de São Paulo)
26. transcript usage from RNA-seq data: isoform pre-ltering improves performance of count-based methods
    Charlotte Soneson, Katarina Luise Matthes, Małgorzata Nowicka, Charity W. Law, Mark D. Robinson · 2015
27. Utilizing Regulatory Networks for Pluripotency Assessment in Stem Cells
    Björn Brändl, Bernhard M. Schuldt, Lena Böhnke, Oliver Keminer, Lea A. I. Vaas, Rainer Fischer, Franz-Josef Müller, Ole Pleß · 2016 · Current Stem Cell Reports
28. Global analysis of gene regulation in mycobacterium bovis (BCG) and streptomyces coelicolor.
    Radhika Pothi · 2016 · Surrey Research Insight Open Access (The University of Surrey)
29. Analysis of Long Noncoding RNAs in RNA-Seq Data
    Farshad Niazi, Saba Valadkhan · 2016 · Springer eBooks
30. Identification of the molecular changes underlying head morphology variation in closely related Drosophila species
    Montserrat Torres-Oliva · 2016
31. Conditional estimation of local pooled dispersion parameter in small-sample RNA-Seq data improves differential expression test
    Jungsoo Gim, Sungho Won, Taesung Park · 2016 · Journal of Bioinformatics and Computational Biology
32. A general workflow for differential expression analysis of RNA-seq and introductions on related tools
    Zhang Zhong · 2016 · International Conference on Electrical & Electronics Engineering and Computer Science (ICEEECS)
33. Small Molecule Biofilm Inhibitors with Antivirulence Properties against Pseudomonas aeruginosa
    Erik van Tilburg Bernardes · 2017 · Libraries and Cultural Resources (University of Calgary)
34. O transcritoma da retinopatia induzida por oxigênio e uma assinatura gênica prognóstica baseada em angiogênese para predição de recidiva de cancer de mama
    Rodrigo Guarischi‐Sousa · 2017
35. Influência do número de repetições na identificação de genes diferencialmente expressos em experimentos de RNA-Seq
    Regiane Teodoro do Amaral, Moysés Nascimento, Talles Eduardo Ferreira Maciel, Fabyano Fonseca e Silva, Ana Carolina Campana Nascimento, Luíz Alexandre Peternelli, Simone Eliza Facioni Guimarães · 2018 · Brazilian Journal of Biometrics
36. Onco-proteogenomic exploration of variant peptide detection in disease models and clinical specimens
    Lampros Dimitrakopoulos · 2017 · TSpace (University of Toronto)
37. Sample size calculations and normalization methods for RNA-seq data.
    Xiaohong Li · 2017
38. Novos reguladores de resposta envolvidos na virulência de Pseudomonas aeruginosa
    Gilberto Hideo Kaihami · 2018
39. Molecular and Synaptic Alterations in the Striatum of GluN1-Deficient Mice
    Yuxiao Chen · 2018 · TSpace (University of Toronto)
40. Application of Next Generation Sequencing and Bioinformatic Approaches to the Study of Influenza Virus Strains and MiRNA Profiling in Liver Diseases
    Zhen Lin · 2016 · ERA: Education and Research Archive (University of Alberta)
41. Peer Review #2 of "Pixel: a content management platform for quantitative omics data (v0.1)"
    2019 · PeerJ
42. Biomarkers of Inflammation and Intestinal Mucosa Pathology in Celiac Disease
    Hanna Gustafsson Bragde · 2019 · Linköping University medical dissertations
43. Peer Review #1 of "Pixel: a content management platform for quantitative omics data (v0.1)"
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44. The role of RNAs and extracellular vesicles in the radiation response
    Laura Ann Jacobs · 2015 · Radar (Oxford Brookes University)
45. Peer Review #1 of "fRNAkenseq: a fully powered-by-CyVerse cloud integrated RNA-sequencing analysis tool (v0.1)"
    2020 · PeerJ
46. Peer Review #2 of "fRNAkenseq: a fully powered-by-CyVerse cloud integrated RNA-sequencing analysis tool (v0.1)"
    2020 · PeerJ
47. Peer Review #2 of "fRNAkenseq: a fully powered-by-CyVerse cloud integrated RNA-sequencing analysis tool (v0.2)"
    2020 · PeerJ
48. Transcriptomics analysis and its applications in cancer
    Alejandra Cervera Taboada · 2020
49. Normalizasyon Yöntemlerinin RNA- Seq Verileri Üzerinde Çıkarılan Gen Birlikte İfade Edilme Ağlarının Performansına Etkisi
    Mustafa Özgür Cingiz · 2021 · Düzce Üniversitesi Bilim ve Teknoloji Dergisi
50. A broad introduction to RNA-Seq
    Felix Richter · 2021 · WikiJournal of Science
51. Computational cancer genomics
    Aman Chandra Kaushik, Shakti Sahi · 2021 · Elsevier eBooks
52. Transcriptomics: Next Generation Transcriptome
    Nicole V. Johnson, Zhong Wang · 2017 · Encyclopedia of Drug Metabolism and Interactions
53. Molecular mechanisms of Yersinia pseudotuberculosis for adaptation and establishment of infection in host tissue
    A. K. M. Firoj Mahmud · 2021 · DiVA at Umeå University (Umeå University)
54. Duesselpore™: a full-stack local web server for rapid and simple analysis of Oxford Nanopore Sequencing data
    Christian Vogeley, Thach Ngoc Nguyen, Selina Woeste, Jean Krutmann, Thomas Haarmann‐Stemmann, Andrea Rossi · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
55. APLIKASI REGISTRASI PASANG BARU PADA PDAM TIRTA MUSI PALEMBANG
    Hollipan Nasir, Cholil Widya, Sa’uda Siti · 2013
56. The Insecticidal Bacterial Toxins in Modern Agriculture
    Juan Ferré, Baltasar Escriche · 2018 · MDPI eBooks
57. Peer Review #2 of "consensusDE: an R package for assessing consensus of multiple RNA-seq algorithms with RUV correction (v0.1)"
    2019 · PeerJ
58. Review for "Oxidative and radiation stress induces transposable elements transcription in Drosophila melanogaster"
    2020 · Publons reviews and discussion
59. Review for "Oxidative and radiation stress induces transposable elements transcription in Drosophila melanogaster"
    2020 · Publons reviews and discussion
60. Peer Review #3 of "Getting the most out of RNA-seq data analysis (v0.1)"
    2015 · PeerJ
61. Peer Review #1 of "consensusDE: an R package for assessing consensus of multiple RNA-seq algorithms with RUV correction (v0.1)"
    2019 · PeerJ
62. Peer Review #1 of "Getting the most out of RNA-seq data analysis (v0.2)"
    2015 · PeerJ
63. Impact of human gene annotations on RNA-seq differential expression analysis
    Yu Hamaguchi, Chao Zeng, Michiaki Hamada · 2021 · Research Square
64. Peer Review #2 of "Getting the most out of RNA-seq data analysis (v0.1)"
    2015 · PeerJ
65. Peer Review #2 of "Getting the most out of RNA-seq data analysis (v0.2)"
    2015 · PeerJ
66. Peer Review #3 of "Getting the most out of RNA-seq data analysis (v0.2)"
    2015 · PeerJ
67. Peer Review #1 of "BingleSeq: a user-friendly R package for bulk and single-cell RNA-Seq data analysis (v0.1)"
    2020 · PeerJ
68. Peer Review #1 of "Getting the most out of RNA-seq data analysis (v0.1)"
    2015 · PeerJ
69. Genomics technologies and bioinformatics in allergy and immunology
    Satishkumar Ranganathan Ganakammal, Ke Qiang Huang, Magdalena A. Walkiewicz, Sandhya Xirasagar · 2022 · Elsevier eBooks
70. Supplementary Methods, Figures 1-6 Supplemental Tables 1-2 from Integrated Genetic, Epigenetic, and Transcriptional Profiling Identifies Molecular Pathways in the Development of Laterally Spreading Tumors
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71. Supplementary Methods, Figures 1-6 Supplemental Tables 1-2 from Integrated Genetic, Epigenetic, and Transcriptional Profiling Identifies Molecular Pathways in the Development of Laterally Spreading Tumors
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72. GEGVIC: A workflow to analyze Gene Expression, Genetic Variations and Immune cell Composition of tumor samples using Next Generation Sequencing data
    Oriol Arqués, Solen Faidherbe, Laia Bassaganyas · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
73. Sample Preparation and Differential Gene Expression Analysis of Human Cancer Cell Lines by RNA Sequencing
    Dmitry R. Leshchiner, Tommy V. Vo, Sachi Horibata · 2023 · Methods in molecular biology
74. TFNetPropX: A Web-Based Comprehensive Analysis Tool for Exploring Condition-Specific RNA-Seq Data Using Transcription Factor Network Propagation
    Ji Hwan Moon, Minsik Oh · 2023 · Applied Sciences
75. Class Discovery, Comparison, and Prediction Methods for RNA-Seq Data
    Ahu Cephe, Necla Koçhan, Gözde Ertürk Zararsız, Vahap Eldem, Gökmen Zararsız · 2023 · IGI Global eBooks
76. Additional file 8 of A comparison of transcriptome analysis methods with reference genome
    Xu Liu, Jialu Zhao, Xue, Liting, Tian Zhao, Wei Ding, Yuying Han, Haihong Ye · 2022 · Figshare
77. Additional file 5 of ROGUE: an R Shiny app for RNA sequencing analysis and biomarker discovery
    Alvin Farrel, Peng Li, Sharon Veenbergen, Khushbu Patel, John M. Maris, Warren J. Leonard · 2023 · Figshare
78. Additional file 2 of Exaggerated false positives by popular differential expression methods when analyzing human population samples
    Yumei Li, Xinzhou Ge, Fanglue Peng, Wei Li, Jingyi Jessica Li · 2022 · Figshare
79. Additional file 9 of A comparison of transcriptome analysis methods with reference genome
    Xu Liu, Jialu Zhao, Xue, Liting, Tian Zhao, Wei Ding, Yuying Han, Haihong Ye · 2022 · Figshare
80. Sensitivity of transcriptomics: Different samples and methodology alter conclusions in Gulf pipefish (Syngnathus scovelli)
    Bernadette D. Johnson, Emily Rose, Adam G. Jones · 2024 · Journal of Heredity
81. Bibliometric Analysis on Methods and Tools Developed for DGE Analysis: Current Trends and Future Perspectives
    Necla Koçhan · 2025 · Yüzüncü Yıl Üniversitesi Fen Bilimleri Enstitüsü Dergisi
82. Quality assessment of differentially expressed gene signatures
    Alexey Stupnikov, Anton A. Buzdin · 2025 · Elsevier eBooks
83. Transcriptomics for modern biotechnology
    Anton A. Buzdin, Denis Kuzmin, Andrew Garazha, Ilya S. Belalov · 2025 · Elsevier eBooks
84. Additional file 2 of MEIRLOP: improving score-based motif enrichment by incorporating sequence bias covariates
    Delos Santos, Nathaniel P., Lorane Texari, Benner, Christopher · 2020 · Figshare
85. Additional file 1 of Exaggerated false positives by popular differential expression methods when analyzing human population samples
    Li, Yumei, Xinzhou Ge, Fanglue Peng, Li, Wei, Li, Jingyi Jessica · 2022 · Figshare
86. Additional file 3 of ROGUE: an R Shiny app for RNA sequencing analysis and biomarker discovery
    Alvin Farrel, Li, Peng, Sharon Veenbergen, Khushbu Patel, Maris, John M., Leonard, Warren J. · 2023 · Figshare
87. Additional file 7 of A comparison of transcriptome analysis methods with reference genome
    Xu Liu, Jialu Zhao, Xue, Liting, Zhao, Tian, Wei Ding, Yuying Han, Ye, Haihong · 2022 · Figshare
88. Additional file 3 of Impact of human gene annotations on RNA-seq differential expression analysis
    Yu Hamaguchi, Chao Zeng, Hamada, Michiaki · 2021 · Figshare
89. Additional file 1 of High heterogeneity undermines generalization of differential expression results in RNA-Seq analysis
    Weitong Cui, Huaru Xue, Wei, Lei, Jin, Jinghua, Tian, Xuewen, Wang, Qinglu · 2021 · Figshare
90. Additional file 1 of MEIRLOP: improving score-based motif enrichment by incorporating sequence bias covariates
    Delos Santos, Nathaniel P., Lorane Texari, Benner, Christopher · 2020 · Figshare
91. Additional file 5 of A comparison of transcriptome analysis methods with reference genome
    Xu Liu, Jialu Zhao, Xue, Liting, Zhao, Tian, Wei Ding, Han, Yuying, Ye, Haihong · 2022 · Figshare
92. Additional file 6 of A comparison of transcriptome analysis methods with reference genome
    Xu Liu, Jialu Zhao, Xue, Liting, Zhao, Tian, Wei Ding, Han, Yuying, Ye, Haihong · 2022 · Figshare
93. Additional file 1 of Impact of human gene annotations on RNA-seq differential expression analysis
    Yu Hamaguchi, Chao Zeng, Hamada, Michiaki · 2021 · Figshare
94. Additional file 3 of Exaggerated false positives by popular differential expression methods when analyzing human population samples
    Li, Yumei, Xinzhou Ge, Fanglue Peng, Li, Wei, Li, Jingyi Jessica · 2022 · Figshare
95. Additional file 3 of A comparison of transcriptome analysis methods with reference genome
    Xu Liu, Jialu Zhao, Xue, Liting, Zhao, Tian, Wei Ding, Yuying Han, Ye, Haihong · 2022 · Figshare
96. Additional file 4 of A comparison of transcriptome analysis methods with reference genome
    Xu Liu, Jialu Zhao, Xue, Liting, Zhao, Tian, Wei Ding, Han, Yuying, Ye, Haihong · 2022 · Figshare
97. Additional file 1 of A transcriptome software comparison for the analyses of treatments expected to give subtle gene expression responses
    Cung Nawl Thawng, Geoffrey Smith · 2022 · Figshare
98. Additional file 4 of ROGUE: an R Shiny app for RNA sequencing analysis and biomarker discovery
    Alvin Farrel, Li, Peng, Sharon Veenbergen, Khushbu Patel, Maris, John M., Leonard, Warren J. · 2023 · Figshare
99. Additional file 4 of High heterogeneity undermines generalization of differential expression results in RNA-Seq analysis
    Weitong Cui, Huaru Xue, Wei, Lei, Jin, Jinghua, Tian, Xuewen, Wang, Qinglu · 2021 · Figshare
100. Additional file 1 of Transcriptome software results show significant variation among different commercial pipelines
     Cung Nawl Thawng, Geoffrey Smith · 2024 · Figshare