Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: cran: SoupX
https://packages.ecosyste.ms/registries/cran.r-project.org/packages/SoupX
Single Cell mRNA Soup eXterminator
6 versions
Latest release: about 2 years ago
1 dependent package
1,030 downloads last month
Papers Mentioning SoupX 17
10.15252/msb.20188746
Current best practices in single‐cell RNA‐seq analysis: a tutorialCited by: 1,173
Author(s): Malte D. Luecken, Fabian J. Theis
Software Mentions: 20
Published: over 5 years ago
10.3389/fgene.2021.689406
Reference Transcriptomes of Porcine Peripheral Immune Cells Created Through Bulk and Single-Cell RNA SequencingCited by: 26
Author(s): Júber Herrera-Uribe, Jayne E Wiarda, Sathesh K Sivasankaran, Lance Daharsh, Haibo Li, Kristen A Byrne, Timothy P. L. Smith, Joan K. Lunney, Crystal L. Loving, Christopher K. Tuggle
Software Mentions: 14
Published: over 3 years ago
10.1126/sciadv.abd3311
Tumor to normal single-cell mRNA comparisons reveal a pan-neuroblastoma cancer cellCited by: 64
Author(s): Gerda Kildisiute, Waleed M. Kholosy, Matthew D. Young, Kenny Roberts, Rasa Elmentaite, Sander R. van Hooff, Clarissa N Pacyna, Eleonora Khabirova, Alice Piapi, Christine Thevanesan, Eva Bugallo-Blanco, Christina Burke, Lira Mamanova, KM Keller, Karin Langenberg-Ververgaert, Philip Lijnzaad, Thanasis Margaritis, Frank C. P. Holstege, Michelle L. Tas, Marc H. W. A. Wijnen, Max M. van Noesel, Ignacio del Valle, Giuseppe Barone, Reinier van der Linden, Catriona Duncan, John Anderson, John C. Achermann, Muzlifah Haniffa, Sarah A. Teichmann, Dyanne Rampling, Neil J. Sebire, Xiaoling He, Ronald R. de Krijger, Roger A. Barker, Kerstin B. Meyer, Ömer Bayraktar, Karin Straathof, Jan J. Molenaar, Sam Behjati
Software Mentions: 8
Published: almost 4 years ago
10.3389/fimmu.2021.711337
Single-Cell RNA Sequencing Identifies New Inflammation-Promoting Cell Subsets in Asian Patients With Chronic PeriodontitisCited by: 17
Author(s): Shu‐Jiao Qian, Qing-Guo Huang, Ruiying Chen, Jia-Ji Mo, Liyun Zhou, Yi Zhao, Bin Li, Hong-Chang Lai
Software Mentions: 8
Published: over 3 years ago
10.15252/emmm.202012871
Integrative analysis of cell state changes in lung fibrosis with peripheral protein biomarkersCited by: 40
Author(s): Christoph H. Mayr, Lukas M. Simon, Gabriela Leuschner, Meshal Ansari, Janine Schniering, Philipp Geyer, Ilias Angelidis, Maximilian Strunz, Pawandeep Singh, Nikolaus Kneidinger, Frank Reichenberger, Edith Silbernagel, Stephan Böhm, Heiko Adler, Michael Lindner, Britta Maurer, Anne Hilgendorff, Antje Prasse, Jürgen Behr, Matthias Mann, Oliver Eickelberg, Fabian J. Theis, Herbert B. Schiller
Software Mentions: 8
Published: almost 4 years ago
10.15252/msb.202110232
Single‐cell analyses reveal SARS‐CoV‐2 interference with intrinsic immune response in the human gutCited by: 64
Author(s): Sergio Triana, Camila Metz-Zumaran, C. Ramı́rez, Carmon Kee, Patricio Doldan, Mohammed Shahraz, Daniel Schraivogel, Andreas R. Gschwind, Ashwini Kumar Sharma, Lars M. Steinmetz, Carl Herrmann, Theodore Alexandrov, Steeve Boulant, Megan L. Stanifer
Software Mentions: 8
Published: over 3 years ago
10.15252/msb.20209442
High‐throughput, microscope‐based sorting to dissect cellular heterogeneityCited by: 40
Author(s): Nicholas Hasle, Anthony Cooke, Sanjay Srivatsan, Heather Z Huang, Jason J. Stephany, Zachary Krieger, Dana L. Jackson, Weiliang Tang, Sriram Pendyala, Raymond J. Monnat, Cole Trapnell, Emily M. Hatch, Douglas M. Fowler
Software Mentions: 7
Published: over 4 years ago
10.3390/jpm11060448
Stromal Heterogeneity in the Human Proliferative Endometrium—A Single-Cell RNA Sequencing StudyCited by: 22
Author(s): Suzanna Queckbörner, Carolina von Grothusen, Nageswara Rao Boggavarapu, Roy Mathew Francis, Lindsay C. Davies, Kristina Gemzell‐Danielsson
Software Mentions: 6
Published: over 3 years ago
10.1016/j.immuni.2020.09.015
Second-Strand Synthesis-Based Massively Parallel scRNA-Seq Reveals Cellular States and Molecular Features of Human Inflammatory Skin PathologiesCited by: 143
Author(s): Travis Hughes, Marc H. Wadsworth, Todd M. Gierahn, Tran Do, David I. Weiss, Priscila Ribeiro Andrade, Feiyang Ma, Bruno Jorge de Andrade Silva, Shuai Shao, Lam C. Tsoi, José Ordovás-Montañés, Jóhann E. Guðjónsson, Robert L. Modlin, J. Christopher Love, Alex K. Shalek
Software Mentions: 6
Published: about 4 years ago
10.7554/eLife.55474
An atlas of cell types in the mouse epididymis and vas deferensCited by: 45
Author(s): Vera D. Rinaldi, Elisa Donnard, Kyle Gellatly, Morten Rasmussen, Alper Küçükural, Onur Yukselen, Manuel Garber, Upasna Sharma, Oliver J. Rando
Software Mentions: 5
Published: over 4 years ago
10.1186/s13059-020-02048-6
Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflowsCited by: 289
Author(s): Elena Denisenko, Belinda Guo, Matthew Jones, Rui Hou, Leanne de Kock, Timo Lassmann, Daniel Poppe, C Olivier, Rebecca K. Simmons, Ryan Lister, Alistair R.R. Forrest
Software Mentions: 5
Published: over 4 years ago
10.1007/s13238-021-00852-9
Single-nucleus transcriptomic landscape of primate hippocampal agingCited by: 41
Author(s): Hui Zhang, Jiaming Li, Jie Ren, Shuhui Sun, Shuai Ma, Weiqi Zhang, Yang Yu, Yusheng Cai, Yan Ke, Wei Li, Baoyang Hu, Piu Chan, Guoguang Zhao, Juan Carlos Izpisúa Belmonte, Qi Zhou, Jing Qu, Si Wang, Guanghui Liu
Software Mentions: 5
Published: over 3 years ago
10.1093/gigascience/giaa151
SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing dataCited by: 438
Author(s): Matthew D. Young, Sam Behjati
Software Mentions: 4
Published: about 4 years ago
10.7554/eLife.56969
Drosophila PDGF/VEGF signaling from muscles to hepatocyte-like cells protects against obesityCited by: 22
Author(s): Arpan C. Ghosh, Sudhir Gopal Tattikota, Yifang Liu, Aram Comjean, Yanhui Hu, Víctor Barrera, Shannan Ho Sui, Norbert Perrimon
Software Mentions: 4
Published: about 4 years ago
10.1007/s13238-020-00705-x
Single-cell transcriptomic analysis of adult mouse pituitary reveals sexual dimorphism and physiologic demand-induced cellular plasticityCited by: 43
Author(s): Yugong Ho, Peng Hu, Michael T. Peel, Sixing Chen, Pablo G. Cámara, Douglas J. Epstein, Hao Wu, Stephen A. Liebhaber
Software Mentions: 3
Published: almost 5 years ago
10.21203/rs.3.rs-846250/v1
Increased Neutrophil-Subset Associated With Severity/Mortality In ARDS And COVID19-ARDS Expresses The Dual Endothelin-1/VEGFsignal-Peptide Receptor (DEspR): An Actionable Therapeutic TargetCited by: 0
Author(s): Victoria L. M. Herrera, Allan J. Walkey, Mai Q. Nguyen, Christopher Gromisch, Julie Z. Mosaddhegi, Matthew S. Gromisch, Bakr Jundi, Soeren Lukassen, Saskia Carstensen, Ridiane Denis, Anna C. Belkina, Rebecca M. Baron, Mayra Pinilla-Vera, Meike Müller, W. Taylor Kimberly, Joshua N. Goldstein, Irina Lehmann, Angela R. Shih, Roland Eils, Bruce D. Levy, Nelson Ruiz-Opazo
Software Mentions: 2
Published: over 3 years ago
10.1172/jci.insight.139793
Obesity results in adipose tissue T cell exhaustionCited by: 47
Author(s): Cara E. Porsche, Jennifer B. DelProposto, Lynn M. Geletka, Robert W. O’Rourke, Carey N. Lumeng
Software Mentions: 2
Published: over 3 years ago