Interpretable single-cell factor decomposition using sciRED
Author
Abstract
Suggested Citation
DOI: 10.1038/s41467-025-57157-2
Download full text from publisher
References listed on IDEAS
- Sonya A. MacParland & Jeff C. Liu & Xue-Zhong Ma & Brendan T. Innes & Agata M. Bartczak & Blair K. Gage & Justin Manuel & Nicholas Khuu & Juan Echeverri & Ivan Linares & Rahul Gupta & Michael L. Cheng, 2018. "Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations," Nature Communications, Nature, vol. 9(1), pages 1-21, December.
- Keren Bahar Halpern & Rom Shenhav & Orit Matcovitch-Natan & Beáta Tóth & Doron Lemze & Matan Golan & Efi E. Massasa & Shaked Baydatch & Shanie Landen & Andreas E. Moor & Alexander Brandis & Amir Gilad, 2017. "Single-cell spatial reconstruction reveals global division of labour in the mammalian liver," Nature, Nature, vol. 542(7641), pages 352-356, February.
- Henry Kaiser, 1958. "The varimax criterion for analytic rotation in factor analysis," Psychometrika, Springer;The Psychometric Society, vol. 23(3), pages 187-200, September.
- Daniel D. Lee & H. Sebastian Seung, 1999. "Learning the parts of objects by non-negative matrix factorization," Nature, Nature, vol. 401(6755), pages 788-791, October.
- Norman Cliff & Roger Pennell, 1967. "The influence of communality, factor strength, and loading size on the sampling characteristics of factor loadings," Psychometrika, Springer;The Psychometric Society, vol. 32(3), pages 309-326, September.
- Jeffrey T Leek & John D Storey, 2007. "Capturing Heterogeneity in Gene Expression Studies by Surrogate Variable Analysis," PLOS Genetics, Public Library of Science, vol. 3(9), pages 1-12, September.
- Xiuwei Zhang & Chenling Xu & Nir Yosef, 2019. "Simulating multiple faceted variability in single cell RNA sequencing," Nature Communications, Nature, vol. 10(1), pages 1-16, December.
- Gastwirth, Joseph L, 1972. "The Estimation of the Lorenz Curve and Gini Index," The Review of Economics and Statistics, MIT Press, vol. 54(3), pages 306-316, August.
- P. M. Hartigan, 1985. "Computation of the Dip Statistic to Test for Unimodality," Journal of the Royal Statistical Society Series C, Royal Statistical Society, vol. 34(3), pages 320-325, November.
- Yue Cao & Pengyi Yang & Jean Yee Hwa Yang, 2021. "A benchmark study of simulation methods for single-cell RNA sequencing data," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
- Keren Bahar Halpern & Rom Shenhav & Orit Matcovitch-Natan & Beáta Tóth & Doron Lemze & Matan Golan & Efi E. Massasa & Shaked Baydatch & Shanie Landen & Andreas E. Moor & Alexander Brandis & Amir Gilad, 2017. "Erratum: Single-cell spatial reconstruction reveals global division of labour in the mammalian liver," Nature, Nature, vol. 543(7647), pages 742-742, March.
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.- Franziska Hildebrandt & Alma Andersson & Sami Saarenpää & Ludvig Larsson & Noémi Van Hul & Sachie Kanatani & Jan Masek & Ewa Ellis & Antonio Barragan & Annelie Mollbrink & Emma R. Andersson & Joakim L, 2021. "Spatial Transcriptomics to define transcriptional patterns of zonation and structural components in the mouse liver," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
- Agnieska Brazovskaja & Tomás Gomes & Rene Holtackers & Philipp Wahle & Christiane Körner & Zhisong He & Theresa Schaffer & Julian Connor Eckel & René Hänsel & Malgorzata Santel & Makiko Seimiya & Timm, 2024. "Cell atlas of the regenerating human liver after portal vein embolization," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
- Brianna R. Watson & Biplab Paul & Raza Ur Rahman & Liat Amir-Zilberstein & Åsa Segerstolpe & Eliana T. Epstein & Shane Murphy & Ludwig Geistlinger & Tyrone Lee & Angela Shih & Jacques Deguine & Ramnik, 2025. "Spatial transcriptomics of healthy and fibrotic human liver at single-cell resolution," Nature Communications, Nature, vol. 16(1), pages 1-16, December.
- Ankit Agrawal & Stefan Thomann & Sukanya Basu & Dominic Grün, 2024. "NiCo identifies extrinsic drivers of cell state modulation by niche covariation analysis," Nature Communications, Nature, vol. 15(1), pages 1-22, December.
- Jie Fang & Shivendra Singh & Changde Cheng & Sivaraman Natarajan & Heather Sheppard & Ahmed Abu-Zaid & Adam D. Durbin & Ha Won Lee & Qiong Wu & Jacob Steele & Jon P. Connelly & Hongjian Jin & Wenan Ch, 2023. "Genome-wide mapping of cancer dependency genes and genetic modifiers of chemotherapy in high-risk hepatoblastoma," Nature Communications, Nature, vol. 14(1), pages 1-27, December.
- Ana Belén Plata-Gómez & Lucía Prado-Rivas & Alba Sanz & Nerea Deleyto-Seldas & Fernando García & Celia Calle Arregui & Camila Silva & Eduardo Caleiras & Osvaldo Graña-Castro & Elena Piñeiro-Yáñez & Jo, 2024. "Hepatic nutrient and hormone signaling to mTORC1 instructs the postnatal metabolic zonation of the liver," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
- Tomaz Martini & Cédric Gobet & Andrea Salati & Jérôme Blanc & Aart Mookhoek & Michael Reinehr & Graham Knott & Jessica Sordet-Dessimoz & Felix Naef, 2024. "A sexually dimorphic hepatic cycle of periportal VLDL generation and subsequent pericentral VLDLR-mediated re-uptake," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
- Zhiyuan Yuan & Yisi Li & Minglei Shi & Fan Yang & Juntao Gao & Jianhua Yao & Michael Q. Zhang, 2022. "SOTIP is a versatile method for microenvironment modeling with spatial omics data," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
- Jingyang Qian & Jie Liao & Ziqi Liu & Ying Chi & Yin Fang & Yanrong Zheng & Xin Shao & Bingqi Liu & Yongjin Cui & Wenbo Guo & Yining Hu & Hudong Bao & Penghui Yang & Qian Chen & Mingxiao Li & Bing Zha, 2023. "Reconstruction of the cell pseudo-space from single-cell RNA sequencing data with scSpace," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
- Thomas A. Kluiver & Yuyan Lu & Stephanie A. Schubert & Lianne J. Kraaier & Femke Ringnalda & Philip Lijnzaad & Jeff DeMartino & Wouter L. Megchelenbrink & Vicky Amo-Addae & Selma Eising & Flavia W. Fa, 2024. "Divergent WNT signaling and drug sensitivity profiles within hepatoblastoma tumors and organoids," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
- Jolene S. Ranek & Wayne Stallaert & J. Justin Milner & Margaret Redick & Samuel C. Wolff & Adriana S. Beltran & Natalie Stanley & Jeremy E. Purvis, 2024. "DELVE: feature selection for preserving biological trajectories in single-cell data," Nature Communications, Nature, vol. 15(1), pages 1-26, December.
- Kristina Handler & Karsten Bach & Costanza Borrelli & Salvatore Piscuoglio & Xenia Ficht & Ilhan E. Acar & Andreas E. Moor, 2023. "Fragment-sequencing unveils local tissue microenvironments at single-cell resolution," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
- Jingyang Qian & Xin Shao & Hudong Bao & Yin Fang & Wenbo Guo & Chengyu Li & Anyao Li & Hua Hua & Xiaohui Fan, 2025. "Identification and characterization of cell niches in tissue from spatial omics data at single-cell resolution," Nature Communications, Nature, vol. 16(1), pages 1-21, December.
- Inmaculada Ruz-Maldonado & John T. Gonzalez & Hanming Zhang & Jonathan Sun & Alicia Bort & Inamul Kabir & Richard G. Kibbey & Yajaira Suárez & Daniel M. Greif & Carlos Fernández-Hernando, 2024. "Heterogeneity of hepatocyte dynamics restores liver architecture after chemical, physical or viral damage," Nature Communications, Nature, vol. 15(1), pages 1-23, December.
- Sun Woo Sophie Kang & Rory P. Cunningham & Colin B. Miller & Lauryn A. Brown & Constance M. Cultraro & Adam Harned & Kedar Narayan & Jonathan Hernandez & Lisa M. Jenkins & Alexei Lobanov & Maggie Cam , 2024. "A spatial map of hepatic mitochondria uncovers functional heterogeneity shaped by nutrient-sensing signaling," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
- Zoe Piran & Mor Nitzan, 2024. "SiFT: uncovering hidden biological processes by probabilistic filtering of single-cell data," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
- Manuel Neumann & Xiaocai Xu & Cezary Smaczniak & Julia Schumacher & Wenhao Yan & Nils Blüthgen & Thomas Greb & Henrik Jönsson & Jan Traas & Kerstin Kaufmann & Jose M. Muino, 2022. "A 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
- Urban Lendahl & Lars Muhl & Christer Betsholtz, 2022. "Identification, discrimination and heterogeneity of fibroblasts," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
- Yuan Guan & Annika Enejder & Meiyue Wang & Zhuoqing Fang & Lu Cui & Shih-Yu Chen & Jingxiao Wang & Yalun Tan & Manhong Wu & Xinyu Chen & Patrik K. Johansson & Issra Osman & Koshi Kunimoto & Pierre Rus, 2021. "A human multi-lineage hepatic organoid model for liver fibrosis," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
- Francesca Lazzeri-Barcelo & Nuria Oliva-Vilarnau & Marion Baniol & Barbara Leibiger & Olaf Bergmann & Volker M. Lauschke & Ingo B. Leibiger & Noah Moruzzi & Per-Olof Berggren, 2024. "Intraocular liver spheroids for non-invasive high-resolution in vivo monitoring of liver cell function," Nature Communications, Nature, vol. 15(1), pages 1-14, 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:16:y:2025:i:1:d:10.1038_s41467-025-57157-2. 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.