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

Ritchie, Matthew E., Phipson, Belinda, Wu, Di, Hu, Yifang, Law, Charity W., Shi, Wei, Smyth, Gordon K.·2015·Nucleic Acids Research

Cited by (649)

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    Zhang, Feng, Zhong, Wenhui, Li, Honghao, Huang, Kaijun, Yu, Min, Liu, Yubin · 2021 · Frontiers in Cell and Developmental Biology
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    Besla, Rickvinder, Penuel, Elicia, Del Rosario, Geoff, Cosino, Ely, Myrta, Szymon, Dillon, Mike, Lazar, Greg A., Nickles, Dorothee, Spiess, Christoph, Yu, Shang-Fan et al. · 2024 · Cancer Immunology Research
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    Kriukov, Dmitrii, Khrameeva, Ekaterina E., Gladyshev, Vadim N., Dmitriev, Sergey E., Tyshkovskiy, Alexander · 2022
  7. Single-cell and spatial detection of senescent cells using DeepScence
    Qu, Yilong, Ji, Beijie, Dong, Runze, Gu, Liangcai, Chan, Cliburn, Xie, Jichun, Glass, Carolyn, Wang, Xiao-Fan, Nixon, Andrew B., Ji, Zhicheng · 2025 · Cell Genomics
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    Tang, Sishi, Liu, Jing, Li, Fangfang, Yan, Yuhan, Long, Xinyi, Fu, Yunfeng · 2024 · Heliyon
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    Murray, Sara A., Dalbøge, Louise S., Baquero, Karalee, Sanford, Christina A., Misquith, Ayesha, Mercer, Aaron J., Meek, Thomas H., Guldbrandt, Mette, Andersen, Birgitte, Kievit, Paul et al. · 2020 · Scientific Reports
  10. Expression quantitative trait locus studies in the era of single-cell omics
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  11. Machine learning with imaging features to predict the expression of ITGAV, which is a poor prognostic factor derived from transcriptome analysis in pancreatic cancer
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    Hsu, Bernadette Y., Driscoll, Julia, Ishida, Yuji, Pino, Cindy, Kim, Eunsun, Zhang, Karen, Tateno, Chise, Mattis, Aras N., Kelley, Robin K., Willenbring, Holger · 2024 · Gastroenterology
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    Luo, Danqing, Yang, Jing, Liu, Junji, Yong, Xia, Wang, Zhimin · 2022 · Hereditas
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    Weber, Claire, Hirst, Marissa B., Ernest, Ben, Schaub, Nicholas J., Wilson, Kelli M., Wang, Ke, Baskir, Hannah M., Chu, Pei-Hsuan, Tristan, Carlos A., Singeç, Ilyas · 2023 · Cell Reports Methods
  15. Controlling for false discoveries subsequently to large scale one‐way ANOVA testing in proteomics: Practical considerations
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  16. Exploring the interaction between T-cell antigen receptor-related genes and MAPT or ACHE using integrated bioinformatics analysis
    Guo, Wenbo, Gou, Xun, Yu, Lei, Zhang, Qi, Yang, Ping, Pang, Minghui, Pang, Xinping, Pang, Chaoyang, Wei, Yanyu, Zhang, XiaoYu · 2023 · Frontiers in Neurology
  17. Comprehensive analysis of MAPK genes in the prognosis, immune characteristics, and drug treatment of renal clear cell carcinoma using bioinformatic analysis and Mendelian randomization
    Zheng, Xinyi, Wang, Yiqiu, Qiu, Xiaoyan · 2024 · European Journal of Pharmacology
  18. Proteomic aging signatures across mouse organs and life stages
    Scifo, Enzo, Morsy, Sarah, Liu, Ting, Xie, Kan, Schaaf, Kristina, Bano, Daniele, Ehninger, Dan · 2025 · The EMBO Journal
  19. Model-based joint visualization of multiple compositional omics datasets
    Hawinkel, Stijn, Bijnens, Luc, Cao, Kim-Anh Lê, Thas, Olivier · 2020 · NAR Genomics and Bioinformatics
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    van der Vliet, Daan, Di, Xinyu, Shamorkina, Tatiana M., Coulon-Bainier, Claire, Pavlovic, Anto, van der Vliet, Iris A. C. M., Zeng, Yingyu, Macnair, Will, van Egmond, Noëlle, Chen, J. Q. Alida et al. · 2026 · Nature Neuroscience
  21. Dietary fish oil enriched in very-long-chain polyunsaturated fatty acid reduces cardiometabolic risk factors and improves retinal function
    Yang, Zhi-Hong, Gorusupudi, Aruna, Lydic, Todd A., Mondal, Anupam K., Sato, Seizo, Yamazaki, Isao, Yamaguchi, Hideaki, Tang, Jingrong, Rojulpote, Krishna Vamsi, Lin, Anna B. et al. · 2023 · iScience
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    Jakobsson, Jenny E., Menezes, Joana, Krock, Emerson, Hunt, Matthew A., Carlsson, Henrik, Vaivade, Aina, Emami Khoonsari, Payam, Agalave, Nilesh M., Sandström, Angelica, Kadetoff, Diana et al. · 2025 · The Journal of Pain
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    Barraza, Gustavo Adolfo, Castro-Guijarro, Ana Carla, de la Fuente Hoffmann, Valentina, Bolívar Ávila, Santiago Junior, Flamini, Marina Inés, Sanchez, Angel Matias · 2024 · Computers in Biology and Medicine
  24. Classifiers for predicting coronary artery disease based on gene expression profiles in peripheral blood mononuclear cells
    Liu, Jie, Wang, Xiaodong, Lin, Junhua, Li, Shaohua, Deng, Guoxiong, Wei, Jinru · 2021 · International Journal of General Medicine
  25. INPP5D/SHIP1 regulates inflammasome activation in human microglia
    Chou, Vicky, Fancher, Seeley B., Pearse, Richard V., Lee, Hyo, Lam, Matti, Seyfried, Nicholas T., Bennett, David A., De Jager, Phillip L., Menon, Vilas, Young-Pearse, Tracy L. · 2023
  26. Prognostic marker identification based on weighted gene co-expression network analysis and associated <i>in vitro</i> confirmation in gastric cancer
    Guo, Haonan, Yang, Jun, Liu, Shanshan, Qin, Tao, Zhao, Qianwen, Hou, Xianliang, Ren, Lei · 2021 · Bioengineered
  27. PLCG2 as a Risk Factor for Alzheimer's Disease.
    Tsai, Andy P., Dong, Chuanpeng, Preuss, Christoph, Moutinho, Miguel, Lin, Peter Bor-Chian, Hajicek, Nicole, Sondek, John, Bissel, Stephanie J., Oblak, Adrian L., Carter, Gregory W. et al. · 2020
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    Dixon, Tom, MacPherson, Derek, Mostofian, Barmak, Dauzhenka, Taras, Lotz, Samuel, McGee, Dwight, Shechter, Sharon, Shrestha, Utsab R., Wiewiora, Rafal, McDargh, Zachary A. et al. · 2021
  29. Developing a Genetic Biomarker-Based Diagnostic Model for Major Depressive Disorder Using Random Forests and Artificial Neural Networks
    Xie, Zhongwen, Gu, Wei, Ming, Tinghong · 2023 · Combinatorial Chemistry &amp; High Throughput Screening
  30. An extended transcription factor regulatory network controls hepatocyte identity
    Dubois‐Chevalier, Julie, Gheeraert, Céline, Berthier, Alexandre, Boulet, Clémence, Dubois, Vanessa, Guille, Loïc, Fourcot, Marie, Marot, Guillemette, Gauthier, Karine, Dubuquoy, Laurent et al. · 2023 · EMBO Reports
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    Huang, Xufeng, Liu, Ying, Wang, Qi, Rehman, Hafiz Muzzammel, Horváth, Dorottya, Zhou, Shujing, Fu, Rao, Zhang, Ling, Szöllősi, Attila Gábor, Li, Zhengrui · 2023 · BMC Oral Health · Retracted
  32. &lt;i&gt;AGTR1&lt;/i&gt;, &lt;i&gt;PLTP&lt;/i&gt;, and &lt;i&gt;SCG2&lt;/i&gt; associated with immune genes and immune cell infiltration in calcific aortic valve stenosis: analysis from integrated bioinformatics and machine learning
    Jiang, Chenyang, Department of Cardiology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China, Jiang, Weidong, Department of Cardiology, Nantong Traditional Chinese Medicine Hospital, Nantong 226001, China · 2022 · Mathematical Biosciences and Engineering
  33. A transcriptomic approach to sex differences in calcific aortic valve stenosis in patients with a tricuspid aortic valve
    Le Nezet, Emma, Tam, Rose, Li, Zhonglin, Gaudreault, Nathalie, Mathieu, Patrick, Côté, Nancy, Guisle, Isabelle, Thériault, Sébastien, Bossé, Yohan, Clavel, Marie-Annick · 2025 · CJC Open
  34. Integrated multi omics and machine learning reveal mitochondrial immunometabolic networks in sepsis associated encephalopathy
    Zhang, Zhenze, Qiu, Xinliang, Zeng, Xing, Liu, Xinhai, Lu, Jiali, Xu, Caixue, Huang, Jing, Zhao, Caiqing, Zhan, Yian · 2025 · Scientific Reports
  35. Reproducible Computational Workflows with Continuous Analysis
    Beaulieu-Jones, Brett K., Greene, Casey S. · 2016
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    Mao, Rui, Li, Ji · 2024 · BMC Medical Genomics
  37. Robust identification of perturbed cell types in single-cell RNA-seq data
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  38. A multiomics approach reveals RNA dynamics promote cellular sensitivity to DNA hypomethylation
    Ge, Alex Y., Arab, Abolfazl, Dai, Raymond, Navickas, Albertas, Fish, Lisa, Garcia, Kristle, Asgharian, Hosseinali, Goudreau, Jackson, Lee, Sean, Keenan, Kathryn et al. · 2024 · Scientific Reports
  39. Functional genomics of trypanotolerant and trypanosusceptible cattle infected with <i>Trypanosoma congolense</i> across multiple time points and tissues
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    Gbelcová, Helena, Rimpelová, Silvie, Jariabková, Adriana, Macášek, Patrik, Priščáková, Petra, Ruml, Tomáš, Šáchová, Jana, Kubovčiak, Jan, Kolář, Michal, Vítek, Libor · 2024 · Scientific Reports
  41. Degron-independent recruitment of KAT2A expands the target space of CRBN molecular glues
    Ojeda, Samuel, Wang, Meng, Baek, Kheewoong, Bourgeois, Wallace, Sommerschield, Alba, Yue, Hong, Metivier, Rebecca J., Karagiannis, Panos, Levitz, Talya S., Xiong, Yuan et al. · 2026 · Science
  42. Multi-omics reveals changes in astrocyte fatty acid metabolism during early stages of Alzheimer's disease
    Zhong, Jie, Li, Manhui, Dai, Ziwei, Wan, Jun · 2025 · Neurochemistry International
  43. Shared and distinct microRNA profiles between HT22, N2A and SH-SY5Y cell lines and primary mouse hippocampal neurons
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  44. Tuberous sclerosis complex‐1 (TSC1) contributes to selective neuronal vulnerability in Alzheimer's disease
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  47. Mitochondrial retrograde control of transcription evolves with respiratory stress, metabolic adaptation, and virulence in budding yeasts
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