scLENS: data-driven signal detection for unbiased scRNA-seq data analysis
Author
Abstract
Suggested Citation
DOI: 10.1038/s41467-024-47884-3
Download full text from publisher
References listed on IDEAS
- Roshan M. Kumar & Patrick Cahan & Alex K. Shalek & Rahul Satija & A. Jay DaleyKeyser & Hu Li & Jin Zhang & Keith Pardee & David Gennert & John J. Trombetta & Thomas C. Ferrante & Aviv Regev & George Q, 2014. "Deconstructing transcriptional heterogeneity in pluripotent stem cells," Nature, Nature, vol. 516(7529), pages 56-61, December.
- George C. Linderman & Jun Zhao & Manolis Roulis & Piotr Bielecki & Richard A. Flavell & Boaz Nadler & Yuval Kluger, 2022. "Zero-preserving imputation of single-cell RNA-seq data," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
- Peng Qiu, 2020. "Embracing the dropouts in single-cell RNA-seq analysis," Nature Communications, Nature, vol. 11(1), pages 1-9, December.
- John Horn, 1965. "A rationale and test for the number of factors in factor analysis," Psychometrika, Springer;The Psychometric Society, vol. 30(2), pages 179-185, June.
- Shahin Mohammadi & Jose Davila-Velderrain & Manolis Kellis, 2020. "A multiresolution framework to characterize single-cell state landscapes," Nature Communications, Nature, vol. 11(1), pages 1-14, December.
- Jong Kyoung Kim & Aleksandra A. Kolodziejczyk & Tomislav Ilicic & Sarah A. Teichmann & John C. Marioni, 2015. "Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression," Nature Communications, Nature, vol. 6(1), pages 1-9, December.
- Zhijian Li & Christoph Kuppe & Susanne Ziegler & Mingbo Cheng & Nazanin Kabgani & Sylvia Menzel & Martin Zenke & Rafael Kramann & Ivan G. Costa, 2021. "Chromatin-accessibility estimation from single-cell ATAC-seq data with scOpen," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
- Duc Tran & Hung Nguyen & Bang Tran & Carlo La Vecchia & Hung N. Luu & Tin Nguyen, 2021. "Fast and precise single-cell data analysis using a hierarchical autoencoder," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
- Koen Van den Berge & Hector Roux de Bézieux & Kelly Street & Wouter Saelens & Robrecht Cannoodt & Yvan Saeys & Sandrine Dudoit & Lieven Clement, 2020. "Trajectory-based differential expression analysis for single-cell sequencing data," Nature Communications, Nature, vol. 11(1), pages 1-13, December.
- Suoqin Jin & Christian F. Guerrero-Juarez & Lihua Zhang & Ivan Chang & Raul Ramos & Chen-Hsiang Kuan & Peggy Myung & Maksim V. Plikus & Qing Nie, 2021. "Inference and analysis of cell-cell communication using CellChat," Nature Communications, Nature, vol. 12(1), pages 1-20, December.
- Wei Vivian Li & Jingyi Jessica Li, 2018. "An accurate and robust imputation method scImpute for single-cell RNA-seq data," Nature Communications, Nature, vol. 9(1), pages 1-9, December.
Most related items
These are the items that most often cite the same works as this one and are cited by the same works as this one.- Lingfei Wang, 2021. "Single-cell normalization and association testing unifying CRISPR screen and gene co-expression analyses with Normalisr," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
- Yichuan Cao & Xiamiao Zhao & Songming Tang & Qun Jiang & Sijie Li & Siyu Li & Shengquan Chen, 2024. "scButterfly: a versatile single-cell cross-modality translation method via dual-aligned variational autoencoders," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
- Songming Tang & Xuejian Cui & Rongxiang Wang & Sijie Li & Siyu Li & Xin Huang & Shengquan Chen, 2024. "scCASE: accurate and interpretable enhancement for single-cell chromatin accessibility sequencing data," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
- Jeff DeMartino & Michael T. Meister & Lindy L. Visser & Mariël Brok & Marian J. A. Groot Koerkamp & Amber K. L. Wezenaar & Laura S. Hiemcke-Jiwa & Terezinha Souza & Johannes H. M. Merks & Anne C. Rios, 2023. "Single-cell transcriptomics reveals immune suppression and cell states predictive of patient outcomes in rhabdomyosarcoma," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
- Benjamin L. Walker & Qing Nie, 2023. "NeST: nested hierarchical structure identification in spatial transcriptomic data," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
- Maxime Brunner & David Lopez-Rodriguez & Judith Estrada-Meza & Rafik Dali & Antoine Rohrbach & Tamara Deglise & Andrea Messina & Bernard Thorens & Federico Santoni & Fanny Langlet, 2024. "Fasting induces metabolic switches and spatial redistributions of lipid processing and neuronal interactions in tanycytes," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
- Malosree Maitra & Haruka Mitsuhashi & Reza Rahimian & Anjali Chawla & Jennie Yang & Laura M. Fiori & Maria Antonietta Davoli & Kelly Perlman & Zahia Aouabed & Deborah C. Mash & Matthew Suderman & Nagu, 2023. "Cell type specific transcriptomic differences in depression show similar patterns between males and females but implicate distinct cell types and genes," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
- Eloise Berson & Anjali Sreenivas & Thanaphong Phongpreecha & Amalia Perna & Fiorella C. Grandi & Lei Xue & Neal G. Ravindra & Neelufar Payrovnaziri & Samson Mataraso & Yeasul Kim & Camilo Espinosa & A, 2023. "Whole genome deconvolution unveils Alzheimer’s resilient epigenetic signature," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
- Sarah Cappuyns & Gino Philips & Vincent Vandecaveye & Bram Boeckx & Rogier Schepers & Thomas Van Brussel & Ingrid Arijs & Aurelie Mechels & Ayse Bassez & Francesca Lodi & Joris Jaekers & Halit Topal &, 2023. "PD-1- CD45RA+ effector-memory CD8 T cells and CXCL10+ macrophages are associated with response to atezolizumab plus bevacizumab in advanced hepatocellular carcinoma," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
- Isaac Dean & Colin Y. C. Lee & Zewen K. Tuong & Zhi Li & Christopher A. Tibbitt & Claire Willis & Fabrina Gaspal & Bethany C. Kennedy & Veronika Matei-Rascu & Rémi Fiancette & Caroline Nordenvall & Ul, 2024. "Rapid functional impairment of natural killer cells following tumor entry limits anti-tumor immunity," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
- Zhuohan Yu & Yanchi Su & Yifu Lu & Yuning Yang & Fuzhou Wang & Shixiong Zhang & Yi Chang & Ka-Chun Wong & Xiangtao Li, 2023. "Topological identification and interpretation for single-cell gene regulation elucidation across multiple platforms using scMGCA," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
- Irfete S. Fetahu & Wolfgang Esser-Skala & Rohit Dnyansagar & Samuel Sindelar & Fikret Rifatbegovic & Andrea Bileck & Lukas Skos & Eva Bozsaky & Daria Lazic & Lisa Shaw & Marcus Tötzl & Dora Tarlungean, 2023. "Single-cell transcriptomics and epigenomics unravel the role of monocytes in neuroblastoma bone marrow metastasis," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
- Maria Lidia Mascia & Mirian Agus & Łukasz Tomczyk & Natale Salvatore Bonfiglio & Diego Bellini & Maria Pietronilla Penna, 2023. "Smartphone Distraction: Italian Validation of the Smartphone Distraction Scale (SDS)," IJERPH, MDPI, vol. 20(15), pages 1-15, August.
- Patrick Hylton & Ben Kisby & Paul Goddard, 2018. "Young People’s Citizen Identities: A Q-Methodological Analysis of English Youth Perceptions of Citizenship in Britain," Societies, MDPI, vol. 8(4), pages 1-21, December.
- Van Acker, Veronique & Ho, Loan & Stevens, Larissa & Mulley, Corinne, 2020. "Quantifying the effects of childhood and previous residential experiences on the use of public transport," Journal of Transport Geography, Elsevier, vol. 86(C).
- Orazio Attanasio & Sarah Cattan & Emla Fitzsimons & Costas Meghir & Marta Rubio-Codina, 2020.
"Estimating the Production Function for Human Capital: Results from a Randomized Controlled Trial in Colombia,"
American Economic Review, American Economic Association, vol. 110(1), pages 48-85, January.
- Orazio Attanasio & Sarah Cattan & Emla Fitzsimons & Costas Meghir & Marta Rubio Codina, 2015. "Estimating the production function for human capital: results from a randomized controlled trial in Colombia," IFS Working Papers W15/06, Institute for Fiscal Studies.
- Orazio Attanasio & Sarah Cattan & Emla Fitzsimons & Costas Meghir & Marta Rubio Codina, 2018. "Estimating the production function for human capital: results from a randomized controlled trial in Colombia," IFS Working Papers W18/18, Institute for Fiscal Studies.
- Orazio Attanasio & Sarah Cattan & Emla Fitzsimons & Costas Meghir & Marta Rubio Codina, 2020. "Estimating the production function for human capital: results from a randomized controlled trial in Colombia," IFS Working Papers W20/3, Institute for Fiscal Studies.
- Orazio Attanasio & Sarah Cattan & Emla Fitzsimons & Costas Meghir & Marta Rubio Codina, 2017. "Estimating the production function for human capital: results from a randomized controlled trial in Colombia," IFS Working Papers W17/06, Institute for Fiscal Studies.
- Yanchuan Li & Huamei Li & Cheng Peng & Ge Meng & Yijun Lu & Honglin Liu & Li Cui & Huan Zhou & Zhu Xu & Lingyun Sun & Lihong Liu & Qing Xiong & Beicheng Sun & Shiping Jiao, 2024. "Unraveling the spatial organization and development of human thymocytes through integration of spatial transcriptomics and single-cell multi-omics profiling," Nature Communications, Nature, vol. 15(1), pages 1-25, December.
- Leiv Gabrielsen & Pål Ulleberg & Reidulf Watten, 2012. "The Adolescent Life Goal Profile Scale: Development of a New Scale for Measurements of Life Goals Among Young People," Journal of Happiness Studies, Springer, vol. 13(6), pages 1053-1072, December.
- Tim Flerlage & Jeremy Chase Crawford & E. Kaitlynn Allen & Danielle Severns & Shaoyuan Tan & Sherri Surman & Granger Ridout & Tanya Novak & Adrienne Randolph & Alina N. West & Paul G. Thomas, 2023. "Single cell transcriptomics identifies distinct profiles in pediatric acute respiratory distress syndrome," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
- Shirong Cao & Yu Pan & Andrew S. Terker & Juan Pablo Arroyo Ornelas & Yinqiu Wang & Jiaqi Tang & Aolei Niu & Sarah Abu Kar & Mengdi Jiang & Wentian Luo & Xinyu Dong & Xiaofeng Fan & Suwan Wang & Matth, 2023. "Epidermal growth factor receptor activation is essential for kidney fibrosis development," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
Corrections
All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-47884-3. See general information about how to correct material in RePEc.
If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.
If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .
If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.
For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .
Please note that corrections may take a couple of weeks to filter through the various RePEc services.