cran: sctransform | Projects | Ecosyste.ms: Papers

10.3389/fimmu.2021.701085

A Single-Cell Atlas of Lymphocyte Adaptive Immune Repertoires and Transcriptomes Reveals Age-Related Differences in Convalescent COVID-19 Patients
Cited by: 29
Author(s): Florian Bieberich, Rodrigo Vazquez-Lombardi, Alexander Yermanos, Roy Ehling, Derek M Mason, Bastian Wagner, Edo Kapetanovic, Raphaël Brisset Di Roberto, Cédric R. Weber, Miodrag Savic, Fabian Rudolf, Sai T. Reddy
Software Mentions: 23
Published: over 3 years ago

10.1186/s13059-020-02136-7

pipeComp, a general framework for the evaluation of computational pipelines, reveals performant single cell RNA-seq preprocessing tools
Cited by: 53
Author(s): Pierre-Luc Germain, Anthony Sonrel, Mark D. Robinson
Software Mentions: 21
Published: over 4 years ago

10.7554/eLife.51254

Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments
Cited by: 102
Author(s): Christopher Jackson, Dayanne M. Castro, Giuseppe-Antonio Saldi, Richard Bonneau, David Gresham
Software Mentions: 20
Published: almost 5 years ago

10.20517/jtgg.2020.51

Toward uncharted territory of cellular heterogeneity: advances and applications of single-cell RNA-seq
Cited by: 2
Author(s): Brandon Lieberman, Meena Kusi, Chia-Nung Hung, Chih-Wei Chou, Ning He, Yen‐Yi Ho, Josephine A. Taverna, Tim Hui-Ming Huang, Chun-Liang Chen
Software Mentions: 18
Published: almost 5 years ago

10.1172/jci.insight.140443

Versatile workflow for cell type–resolved transcriptional and epigenetic profiles from cryopreserved human lung
Cited by: 6
Author(s): Maria Llamazares Prada, Elisa Espinet, Vedrana Mijošek, Uwe Schwartz, Pavlo Lutsik, Raluca Tamas, Mandy Richter, Annika Behrendt, Stephanie Pohl, Naja P. Benz, Thomas Muley, Arne Warth, Claus Peter Heusel, Hauke Winter, Jonathan Landry, Felix J.F. Herth, Tinne Mertens, Harry Karmouty‐Quintana, Ina Koch, Vladimı́r Beneš, Jan O. Korbel, Sebastian M. Waszak, Andreas Trumpp, David Wyatt, Heiko Stahl, Christoph Plass, Renata Z. Jurkowska
Software Mentions: 9
Published: almost 4 years ago

10.1186/s13059-020-02096-y

Demystifying “drop-outs” in single-cell UMI data
Cited by: 66
Author(s): Tae Hyun Kim, Xiang Zhou, Mengjie Chen
Software Mentions: 9
Published: over 4 years ago

10.1186/s13059-021-02407-x

Optimizing expression quantitative trait locus mapping workflows for single-cell studies
Cited by: 30
Author(s): Anna Cuomo, Giordano Alvari, Christina B. Azodi, Davis J. McCarthy, Marc Jan Bonder
Software Mentions: 9
Published: over 3 years ago

10.7554/eLife.69065

Cross-species analysis defines the conservation of anatomically segregated VMH neuron populations
Cited by: 16
Author(s): Alison H. Affinati, Paul V. Sabatini, Cadence True, Abigail J. Tomlinson, Melissa A. Kirigiti, Sarah R. Lindsley, Chien Li, David P. Olson, Paul Kievit, Martin G. Myers, Alan C. Rupp
Software Mentions: 8
Published: over 3 years ago

10.15252/msb.202110232

Single‐cell analyses reveal SARS‐CoV‐2 interference with intrinsic immune response in the human gut
Cited 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: almost 4 years ago

10.7554/eLife.65445

Molecular characterization of projection neuron subtypes in the mouse olfactory bulb
Cited by: 16
Author(s): Sara Zeppilli, Tobias Ackels, Robin Attey, Nell Klimpert, Kimberly Ritola, Stefan Boeing, Anton Crombach, Andreas T. Schaefer, Alexander Fleischmann
Software Mentions: 8
Published: over 3 years ago

10.15252/msb.202010060

CASB: a concanavalin A‐based sample barcoding strategy for single‐cell sequencing
Cited by: 11
Author(s): Liang Fang, Guipeng Li, Zhiyuan Sun, Qionghua Zhu, Huanhuan Cui, Yunfei Li, Jingwen Zhang, Weizheng Liang, Wencheng Wei, Yuhui Hu, Wei Chen
Software Mentions: 8
Published: almost 4 years ago

10.1016/j.celrep.2021.108990

Stabilized epithelial phenotype of cancer cells in primary tumors leads to increased colonization of liver metastasis in pancreatic cancer
Cited by: 39
Author(s): Julienne L. Carstens, Stephen C. Yang, Pedro Corrêa de Sampaio, Xiaofeng Zheng, Souptik Barua, Kathleen M. McAndrews, Arvind Rao, Jared K. Burks, Andrew D. Rhim, Raghu Kalluri
Software Mentions: 6
Published: almost 4 years ago

10.3390/jpm11060448

Stromal Heterogeneity in the Human Proliferative Endometrium—A Single-Cell RNA Sequencing Study
Cited 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

10.15252/msb.20209833

Single‐cell transcriptomics reveals immune response of intestinal cell types to viral infection
Cited by: 17
Author(s): Sergio Triana, Megan L. Stanifer, Camila Metz-Zumaran, Mohammed Shahraz, Markus Mukenhirn, Carmon Kee, Clara Serger, Ronald Koschny, Diana Ordoñez-Rueda, Malte Paulsen, Vladimı́r Beneš, Steeve Boulant, Theodore Alexandrov
Software Mentions: 6
Published: over 3 years ago

10.1186/s13059-019-1806-0

scBFA: modeling detection patterns to mitigate technical noise in large-scale single-cell genomics data
Cited by: 15
Author(s): Ruoxin Li, Gerald Quon
Software Mentions: 6
Published: over 5 years ago

10.1186/s13059-019-1874-1

Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression
Cited by: 2,100
Author(s): Christoph Hafemeister, Rahul Satija
Software Mentions: 6
Published: about 5 years ago

10.1186/s12915-021-01034-z

Single-cell transcriptomics reveals the effect of PD-L1/TGF-β blockade on the tumor microenvironment
Cited by: 14
Author(s): Yoong Wearn Lim, Garry L. Coles, Savreet K. Sandhu, D. S. Johnson, Adam S. Adler, Erica L. Stone
Software Mentions: 6
Published: over 3 years ago

10.1172/jci.insight.144294

The MUC5B-associated variant rs35705950 resides within an enhancer subject to lineage- and disease-dependent epigenetic remodeling
Cited by: 20
Author(s): Fabienne Gally, Sarah K. Sasse, Jonathan S. Kurche, Margaret Gruca, Jonathan Cardwell, Tsukasa Okamoto, Hong Wei Chu, Xiaomeng Hou, Olivier Poirion, Justin Buchanan, Sebastian Preißl, Bing Ren, Sean P. Colgan, Robin D. Dowell, Ivana V. Yang, David A. Schwartz, Anthony N. Gerber
Software Mentions: 5
Published: almost 4 years ago

10.1016/j.medj.2021.01.006

Identifying CNS-colonizing T cells as potential therapeutic targets to prevent progression of multiple sclerosis
Cited by: 39
Author(s): Max Kaufmann, Hayley G. Evans, Anna-Lena Schaupp, Jan Broder Engler, Gurman Kaur, Anne Willing, Nina Kursawe, Charlotte Schubert, Kathrine E. Attfield, Lars Fugger, Manuel A. Friese
Software Mentions: 5
Published: almost 4 years ago

10.1186/s13395-021-00269-2

Single cell RNA-seq analysis of the flexor digitorum brevis mouse myofibers
Cited by: 5
Author(s): Rohan Verma, Suraj Kannan, Brian L. Lin, Katherine M. Fomchenko, Tim O. Nieuwenhuis, Arun H. Patil, Clarisse Lukban, Xiao‐Ping Yang, Karen Fox-Talbot, Matthew N. McCall, Chulan Kwon, David A. Kass, Avi Rosenberg, Marc K. Halushka
Software Mentions: 4
Published: over 3 years ago

10.1038/s42003-020-01463-6

Transfer learning efficiently maps bone marrow cell types from mouse to human using single-cell RNA sequencing
Cited by: 15
Author(s): Patrick S. Stumpf, Xin Du, Haruka Imanishi, Yuya Kunisaki, Yuichiro Semba, Timothy J. Noble, R Smith, Matthew Rose-Zerili, Jonathan West, Richard O.C. Oreffo, Katayoun Farrahi, Mahesan Niranjan, Koichi Akashi, Fumio Arai, Ben D. MacArthur
Software Mentions: 4
Published: about 4 years ago

10.1186/s13024-021-00423-w

Methods to investigate intrathecal adaptive immunity in neurodegeneration
Cited by: 11
Author(s): Hamilton Oh, Olivia Leventhal, Divya Channappa, Victor W. Henderson, Tony Wyss‐Coray, Benoit Lehallier, David Gate
Software Mentions: 4
Published: almost 4 years ago

10.1128/mBio.01959-21

Multifactorial Role of Mitochondria in Echinocandin Tolerance Revealed by Transcriptome Analysis of Drug-Tolerant Cells
Cited by: 13
Author(s): Rocio Garcia-Rubio, Cristina Jiménez‐Ortigosa, Lucius DeGregorio, Christopher Quinteros, Erika Shor, David S. Perlin
Software Mentions: 4
Published: over 3 years ago

10.3389/fncel.2021.624826

Single Cell Transcriptome Data Analysis Defines the Heterogeneity of Peripheral Nerve Cells in Homeostasis and Regeneration
Cited by: 28
Author(s): Bing Chen, Matthew C. Banton, Lolita Singh, David B. Parkinson, Xin‐Peng Dun
Software Mentions: 3
Published: almost 4 years ago

10.1074/jbc.RA120.015679

Danish and British dementia ITM2b/BRI2 mutations reduce BRI2 protein stability and impair glutamatergic synaptic transmission
Cited by: 16
Author(s): Tao Yin, Wen Yao, Alexander Lemenze, Luciano D’Adamio
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pbio.3000421

Adult bone marrow progenitors become decidual cells and contribute to embryo implantation and pregnancy
Cited by: 44
Author(s): Reshef Tal, Shafiq Shaikh, Pallavi Pallavi, Aya Tal, Francesc López-Giráldez, Fang Lyu, Yuanyuan Fang, Shruti Chinchanikar, Ying Liu, Harvey J. Kliman, Myles H. Alderman, Nicola Pluchino, Jehanzeb Kayani, Ramanaiah Mamillapalli, Diane S. Krause, Hugh S. Taylor
Software Mentions: 3
Published: over 5 years ago

10.1172/jci.insight.141618

Loss of Fas signaling in fibroblasts impairs homeostatic fibrosis resolution and promotes persistent pulmonary fibrosis
Cited by: 25
Author(s): Elizabeth F. Redente, Sangeeta Chakraborty, Satria Sajuthi, Bart P. Black, Benjamin Edelman, Max A. Seibold, David W. H. Riches
Software Mentions: 3
Published: about 4 years ago

10.1186/s13059-020-02171-4

RNA editing in cancer impacts mRNA abundance in immune response pathways
Cited by: 26
Author(s): Tracey W. Chan, Ting Fu, Jae Hoon Bahn, Hyun-Ik Jun, Jae‐Hyung Lee, Giovanni Quinones-Valdez, Chonghui Cheng, Xinshu Xiao
Software Mentions: 2
Published: about 4 years ago

10.1186/s40364-020-00253-w

Longitudinal CITE-Seq profiling of chronic lymphocytic leukemia during ibrutinib treatment: evolution of leukemic and immune cells at relapse
Cited by: 14
Author(s): Sarah Cadot, Carine Valle, Marie Tosolini, Frédéric Pont, Laëtitia Largeaud, Camille Laurent, Jean Jacques Fourniè, Loïc Ysebaert, Anne Quillet‐Mary
Software Mentions: 2
Published: about 4 years ago

10.1186/s12859-020-03797-8

Impact of data preprocessing on cell-type clustering based on single-cell RNA-seq data
Cited by: 9
Author(s): Chunxiang Wang, Xin Gao, Juntao Liu
Software Mentions: 2
Published: about 4 years ago

10.1186/s13073-021-00941-8

Using single-nucleus RNA-sequencing to interrogate transcriptomic profiles of archived human pancreatic islets
Cited by: 14
Author(s): Giorgio Basile, Sevim Kahraman, Ercument Dirice, Pei Hui, Jonathan M. Dreyfuss, Rohit Kulkarni
Software Mentions: 2
Published: over 3 years ago

10.1172/jci.insight.142513

PD-1 blockade restores helper activity of tumor-infiltrating, exhausted PD-1hiCD39+ CD4 T cells
Cited by: 58
Author(s): Camille-Charlotte Balança, Anna Salvioni, Clara-Maria Scarlata, Marie Michelas, Carlos Martínez-Gómez, Carlos Gomez‐Roca, Victor Sarradin, Marie Tosolini, Carine Valle, Frédéric Pont, Gwénaël Ferron, Laurence Gladieff, S. Vergez, Agnès Dupret‐Bories, Eliane Mery-Lamarche, Philippe Rochaix, Jean‐Jacques Fournié, Jean‐Pierre Delord, Christel Devaud, Alejandra Martínez, Maha Ayyoub
Software Mentions: 2
Published: almost 4 years ago

10.1093/ecco-jcc/jjaa054

Lymphocyte Activation Gene (LAG)-3 Is Associated With Mucosal Inflammation and Disease Activity in Ulcerative Colitis
Cited by: 20
Author(s): Stephanie Slevin, Lucy C. Garner, Conor Lahiff, Min Tan, L M Wang, Helen Ferry, Borgel Greenaway, Kate D. Lynch, A Geremia, Stephen A. Hughes, Karen Leavens, David Krull, Marks Djb., Katherine Nevin, Kevin Page, Naren Srinivasan, Ruth M. Tarzi, Paul Klenerman, Simon Travis, Carolina V. Arancibia‐Cárcamo, Satish Keshav
Software Mentions: 2
Published: almost 5 years ago

10.1155/2021/6619302

Identification of the Different Gene Expression Characteristics from Liver Cirrhosis to Hepatocellular Carcinoma Using Single-Cell Sequencing Analyses
Cited by: 5
Author(s): Xin Xing, Jian Song
Software Mentions: 2
Published: almost 4 years ago

Ecosyste.ms: Papers

Projects: cran: sctransform

Papers Mentioning sctransform 34