bioconductor: scater | Projects | Ecosyste.ms: Papers

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: about 4 years ago

10.1371/journal.pcbi.1006361

scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data
Cited by: 92
Author(s): Tian Li, Shian Su, Xueyi Dong, Daniela Amann‐Zalcenstein, Christine Biben, Azadeh Seidi, Douglas J. Hilton, Shalin H. Naik, Matthew E. Ritchie
Software Mentions: 21
Published: about 6 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

10.12688/f1000research.15666.3

A systematic performance evaluation of clustering methods for single-cell RNA-seq data
Cited by: 33
Author(s): Angelo Duò, Mark D. Robinson, Charlotte Soneson
Software Mentions: 17
Published: almost 4 years ago

10.1371/journal.pcbi.1006245

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database
Cited by: 213
Author(s): Luke Zappia, Belinda Phipson, Alicia Oshlack
Software Mentions: 17
Published: over 6 years ago

10.1126/sciimmunol.abd6832

Natural killer cell immunotypes related to COVID-19 disease severity
Cited by: 315
Author(s): Christopher Maucourant, Iva Filipovic, Andrea Ponzetta, Soo Aleman, Martin Cornillet, Laura Hertwig, Benedikt Strunz, Antonio Lentini, Björn Reinius, Demi Brownlie, Angélica Cuapio, Eivind Heggernes Ask, Ryan M. Hull, Alvaro Haroun-Izquierdo, Marie Schaffer, Jonas Klingström, Elin Folkesson, Marcus Buggert, Johan K. Sandberg, Lars Eriksson, Olav Rooyackers, Hans‐Gustaf Ljunggren, Karl‐Johan Malmberg, Jakob Michaëlsson, Nicole Marquardt, Quirin Hammer, Kristoffer Strålin, Niklas K. Björkström
Software Mentions: 16
Published: about 4 years ago

10.1371/journal.pcbi.1008625

mbkmeans: Fast clustering for single cell data using mini-batch k-means
Cited by: 27
Author(s): Stephanie C. Hicks, Ruoxi Liu, Yuwei Ni, Elizabeth Purdom, Davide Risso
Software Mentions: 15
Published: almost 4 years ago

10.1002/1873-3468.12684

Computational approaches for interpreting sc <scp>RNA</scp> ‐seq data
Cited by: 111
Author(s): Raghd Rostom, Valentine Svensson, Sarah A. Teichmann, Gozde Kar
Software Mentions: 14
Published: over 7 years ago

10.1093/bioinformatics/btw777

Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R
Cited by: 1,059
Author(s): Davis J. McCarthy, Kieran R Campbell, Aaron T. L. Lun, Quin F. Wills
Software Mentions: 14
Published: almost 8 years ago

10.1186/s40478-020-0880-6

Single-nucleus RNA-seq identifies Huntington disease astrocyte states
Cited by: 147
Author(s): Osama Al‐Dalahmah, Alexander A. Sosunov, Ayesha Shaik, Kenneth Ofori, Yang Liu, Jean Paul Vonsattel, István Adorján, Vilas Menon, James E. Goldman
Software Mentions: 14
Published: over 4 years ago

10.1186/s13059-019-1898-6

Accuracy, robustness and scalability of dimensionality reduction methods for single-cell RNA-seq analysis
Cited by: 123
Author(s): Shuang Sun, Jiaqiang Zhu, Ying Ma, Xiang Zhou
Software Mentions: 13
Published: almost 5 years ago

10.1186/s13059-017-1305-0

Splatter: simulation of single-cell RNA sequencing data
Cited by: 575
Author(s): Luke Zappia, Belinda Phipson, Alicia Oshlack
Software Mentions: 13
Published: about 7 years ago

10.1186/s13059-019-1739-7

CellSIUS provides sensitive and specific detection of rare cell populations from complex single-cell RNA-seq data
Cited by: 33
Author(s): Rebekka Wegmann, Marilisa Neri, Sven Schuierer, Bilada Bilican, Huyen Hartkopf, Florian Nigsch, Felipa Mapa, Annick Waldt, Rachel Cuttat, Max R. Salick, Joe Raymond, Ajamete Kaykas, Guglielmo Roma, Caroline Gubser Keller
Software Mentions: 13
Published: over 5 years ago

10.12688/f1000research.15809.2

Comparison of clustering tools in R for medium-sized 10x Genomics single-cell RNA-sequencing data
Cited by: 90
Author(s): Saskia Freytag, Tian Li, Ingrid Lönnstedt, Milica Ng, Melanie Bahlo
Software Mentions: 12
Published: almost 6 years ago

10.26508/lsa.202001004

CellMixS: quantifying and visualizing batch effects in single-cell RNA-seq data
Cited by: 21
Author(s): Almut Luetge, Joanna Zyprych-Walczak, Urszula Brykczynska Kunzmann, Helena L. Crowell, Daniela Calini, Dheeraj Malhotra, Charlotte Soneson, Mark D. Robinson
Software Mentions: 12
Published: over 3 years ago

10.3389/fgene.2019.01200

Dysregulation of MicroRNA Regulatory Network in Lower Extremities Arterial Disease
Cited by: 22
Author(s): Anna Bogucka‐Kocka, Daniel Zalewski, Karol P Ruszel, Andrzej Stępniewski, Dariusz Gałkowski, Jacek Bogucki, Łukasz Komsta, Przemysław Kołodziej, Tomasz Zubilewicz, Marcin Feldo, Janusz Kocki
Software Mentions: 12
Published: almost 5 years ago

10.7554/eLife.38579

FoxA1 and FoxA2 drive gastric differentiation and suppress squamous identity in NKX2-1-negative lung cancer
Cited by: 52
Author(s): Soledad A. Camolotto, S. R. Pattabiraman, Timothy Mosbruger, Alex Jones, Veronika K Belova, Grace Orstad, Mitchell Streiff, Lydia Salmond, Chris Stubben, Klaus H. Kaestner, Eric L. Snyder
Software Mentions: 12
Published: almost 6 years ago

10.12688/f1000research.9501.2

A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor
Cited by: 693
Author(s): Aaron T. L. Lun, Davis J. McCarthy, John C. Marioni
Software Mentions: 12
Published: about 8 years ago

10.12688/f1000research.12122.1

Bioconductor workflow for single-cell RNA sequencing: Normalization, dimensionality reduction, clustering, and lineage inference
Cited by: 14
Author(s): Fanny Perraudeau, Davide Risso, Kelly Street, Elizabeth Purdom, Sandrine Dudoit
Software Mentions: 12
Published: over 7 years ago

10.1371/journal.pcbi.1008585

Preprocessing choices affect RNA velocity results for droplet scRNA-seq data
Cited by: 43
Author(s): Charlotte Soneson, Avi Srivastava, Rob Patro, Michael Stadler
Software Mentions: 11
Published: almost 4 years ago

10.1016/j.cell.2018.08.067

Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease
Cited by: 396
Author(s): James Kinchen, Hannah H. Chen, Kaushal Parikh, Agne Antanaviciute, Marta Jagielowicz, David Fawkner-Corbett, Neil Ashley, Laura Cubitt, Esther Mellado-Gomez, Moustafa Attar, Eshita Sharma, Quin F. Wills, Rory Bowden, Felix Clemens Richter, David Ahern, Kamal D. Puri, Jill Hénault, François G. Gervais, Hashem Koohy, Alison Simmons
Software Mentions: 11
Published: about 6 years ago

10.1016/j.celrep.2019.05.026

ZIC3 Controls the Transition from Naive to Primed Pluripotency
Cited by: 41
Author(s): Shen Hsi Yang, Munazah Andrabi, Rebecca Biss, Syed Murtuza Baker, Mudassar Iqbal, Andrew D. Sharrocks
Software Mentions: 11
Published: over 5 years ago

10.1371/journal.pcbi.1006135

beachmat: A Bioconductor C++ API for accessing high-throughput biological data from a variety of R matrix types
Cited by: 13
Author(s): Aaron T. L. Lun, Hervé Pagès, Mike L. Smith
Software Mentions: 10
Published: over 6 years ago

10.1038/s42003-020-0842-3

Loss of the branched-chain amino acid transporter CD98hc alters the development of colonic macrophages in mice
Cited by: 17
Author(s): Philipp Wuggenig, Berna Kaya, Hassan Melhem, C. Korcan Ayata, Swiss Ibd Cohort Investigators, Petr Hrúz, Emre Sayan, Hideki Tsumura, Morihiro Ito, Julien Roux, Jan Hendrik Niess
Software Mentions: 10
Published: over 4 years ago

10.1016/j.celrep.2019.10.024

Single-Cell Transcriptomics Uncovers Zonation of Function in the Mesenchyme during Liver Fibrosis
Cited by: 227
Author(s): Ross Dobie, John Wilson-Kanamori, Beth E. P. Henderson, J. F. Smith, Kylie P. Matchett, Jordan Raymond Portman, Karolina Wallenborg, Simone Picelli, Анна Загорска, Swetha Pendem, Thomas E. Hudson, Max C. Wu, Grant R. Budas, David G. Breckenridge, Ewen M Harrison, Damian J. Mole, Stephen J. Wigmore, Prakash Ramachandran, Chris P. Ponting, Sarah A. Teichmann, John C. Marioni, Neil C. Henderson
Software Mentions: 10
Published: about 5 years ago

10.1016/j.celrep.2020.108661

Human intestinal tissue-resident memory T cells comprise transcriptionally and functionally distinct subsets
Cited by: 47
Author(s): Michael Fitzpatrick, Nicholas M. Provine, Lucy C. Garner, Kate Powell, Ali Amini, Sophie Irwin, Helen Ferry, Tim Ambrose, Peter J. Friend, Georgios Vrakas, Srikanth Reddy, Elizabeth Soilleux, Paul Klenerman, Philip Allan
Software Mentions: 9
Published: almost 4 years ago

10.1186/s13059-019-1662-y

EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data
Cited by: 518
Author(s): Aaron T. L. Lun, Samantha J. Riesenfeld, Tallulah Andrews, Tomás Gomes, John C. Marioni
Software Mentions: 9
Published: over 5 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

10.3389/fgene.2019.01253

Benchmark and Parameter Sensitivity Analysis of Single-Cell RNA Sequencing Clustering Methods
Cited by: 56
Author(s): Monika Krzak, Yordan P. Raykov, Alexis Boukouvalas, Luisa Cutillo, Claudia Angelini
Software Mentions: 9
Published: almost 5 years ago

10.1371/journal.pone.0210571

Deterministic column subset selection for single-cell RNA-Seq
Cited by: 0
Author(s): Shannon R. McCurdy, Vasilis Ntranos, Lior Pachter
Software Mentions: 8
Published: almost 6 years ago

10.1038/s42003-021-02146-6

NEBULA is a fast negative binomial mixed model for differential or co-expression analysis of large-scale multi-subject single-cell data
Cited by: 38
Author(s): Liyun He, José Dávila-Velderrain, Tomokazu Sumida, David A. Hafler, M Kellis, Alexander M. Kulminski
Software Mentions: 8
Published: over 3 years ago

10.3389/fcvm.2018.00167

Single Cell Gene Expression to Understand the Dynamic Architecture of the Heart
Cited by: 15
Author(s): Andrea Massaia, Patrícia Chaves, Sara Samari, Ricardo J. Miragaia, Kerstin B. Meyer, Sarah A. Teichmann, Michela Noseda
Software Mentions: 8
Published: almost 6 years ago

10.3389/fgene.2021.665843

RFCell: A Gene Selection Approach for scRNA-seq Clustering Based on Permutation and Random Forest
Cited by: 3
Author(s): Yuan Zhao, Zhao-Yu Fang, Cui-Xiang Lin, Chao Deng, Yunpei Xu, Hongdong Li
Software Mentions: 8
Published: over 3 years ago

10.1186/s13073-019-0615-0

Single-cell analysis reveals congruence between kidney organoids and human fetal kidney
Cited by: 144
Author(s): Alexander N. Combes, Luke Zappia, Pei X. Er, Alicia Oshlack, Melissa H. Little
Software Mentions: 8
Published: almost 6 years ago

10.1371/journal.pcbi.1009290

miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data
Cited by: 23
Author(s): Ariel A. Hippen, Matías M. Falco, Lukas M. Weber, Erdoğan Pekcan Erkan, Kaiyang Zhang, Jennifer A. Doherty, Anna Vähärautio, Casey S. Greene, Stephanie C. Hicks
Software Mentions: 7
Published: about 3 years ago

10.1186/s13059-019-1639-x

CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA sequencing
Cited by: 23
Author(s): K. Sato, Koki Tsuyuzaki, Kentaro Shimizu, Itoshi Nikaido
Software Mentions: 7
Published: over 5 years ago

10.1016/j.isci.2021.102870

Single paternal dexamethasone challenge programs offspring metabolism and reveals multiple candidates in RNA-mediated inheritance
Cited by: 14
Author(s): Katharina Gapp, Guillermo E. Parada, Fridolin Groß, Alberto Corcoba, Jasmine Kaur, Evelyn Grau, Martin Hemberg, Johannes Bohacek, Eric A. Miska
Software Mentions: 7
Published: over 3 years ago

10.3389/fcimb.2021.604129

Using scRNA-seq to Identify Transcriptional Variation in the Malaria Parasite Ookinete Stage
Cited by: 6
Author(s): Kathrin Witmer, Farah A. Dahalan, Tom Metcalf, Arthur M. Talman, Virginia M. Howick, Mara K. N. Lawniczak
Software Mentions: 7
Published: over 3 years ago

10.7554/eLife.53360

Dual histone methyl reader ZCWPW1 facilitates repair of meiotic double strand breaks in male mice
Cited by: 25
Author(s): Mohamed Mahgoub, Jacob Paiano, Melania Bruno, Wei Wu, Sarath Pathuri, Xing Zhang, Sherry Ralls, Xiaodong Cheng, André Nussenzweig, Todd S. Macfarlan
Software Mentions: 7
Published: over 4 years ago

10.1016/j.cell.2021.01.002

Meta-analysis of tumor- and T cell-intrinsic mechanisms of sensitization to checkpoint inhibition
Cited by: 412
Author(s): Kevin Litchfield, James L. Reading, Clare Puttick, Krupa Thakkar, Chris Abbosh, Robert Bentham, Thomas B.K. Watkins, Rachel Rosenthal, Dhruva Biswas, Andrew Rowan, Emilia L. Lim, Maise Al Bakir, Virginia Turati, José Afonso Guerra-Assunção, Lucía Conde, Andrew J.S. Furness, Sunil Kumar Saini, Sine Reker Hadrup, Javier Herrero, Se‐Hoon Lee, Peter Van Loo, Tariq Enver, James Larkin, Matthew D. Hellmann, Samra Turajlic, Sergio A. Quezada, Nicholas McGranahan, Charles Swanton
Software Mentions: 7
Published: almost 4 years ago

10.12688/f1000research.11290.1

Gene length and detection bias in single cell RNA sequencing protocols
Cited by: 71
Author(s): Belinda Phipson, Luke Zappia, Alicia Oshlack
Software Mentions: 7
Published: over 7 years ago

10.3389/fimmu.2018.01553

Single Cell RNA Sequencing of Rare Immune Cell Populations
Cited by: 88
Author(s): Akira Nguyen, Weng Hua Khoo, Imogen Moran, Peter I. Croucher, Tri Giang Phan
Software Mentions: 7
Published: over 6 years ago

10.7554/eLife.43696

Complementary networks of cortical somatostatin interneurons enforce layer specific control
Cited by: 82
Author(s): Alexander Naka, Julia Veit, Ben Shababo, Rebecca K. Chance, Davide Risso, David Stafford, Benjamin Snyder, Andrew Egladyous, Desiree Chu, Savitha Sridharan, Daniel P. Mossing, Liam Paninski, John Ngai, Hillel Adesnik
Software Mentions: 7
Published: over 5 years ago

10.1093/gigascience/giz087

ascend: R package for analysis of single-cell RNA-seq data
Cited by: 35
Author(s): Anne Senabouth, Samuel W. Lukowski, Jose Alquicira Hernandez, Stacey Andersen, Xin Mei, Quan Nguyen, Joseph E. Powell
Software Mentions: 7
Published: over 5 years ago

10.1016/j.celrep.2020.03.063

A Targeted Multi-omic Analysis Approach Measures Protein Expression and Low-Abundance Transcripts on the Single-Cell Level
Cited by: 71
Author(s): Florian Mair, Jami R. Erickson, Valentin Voillet, Yannick Simoni, Timothy Bi, Aaron J. Tyznik, Jody Martin, Raphaël Gottardo, Evan W. Newell, Martin Prlic
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pgen.1007788

Single-cell RNA-sequencing reveals transcriptional dynamics of estrogen-induced dysplasia in the ovarian surface epithelium
Cited by: 16
Author(s): Nhung Vuong, David P. Cook, Laura A. Forrest, Lauren E. Carter, Pascale Robineau-Charette, Joshua M. Kofsky, Kendra M. Hodgkinson, Barbara C. Vanderhyden
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pbio.3001077

Cell-level metadata are indispensable for documenting single-cell sequencing datasets
Cited by: 5
Author(s): Sidhant Puntambekar, Jay R. Hesselberth, Kent Riemondy, Rui Fu
Software Mentions: 6
Published: over 3 years ago

10.26508/lsa.202000707

Robust production of uniform human cerebral organoids from pluripotent stem cells
Cited by: 44
Author(s): Adam Sivitilli, Jessica Gosio, Bibaswan Ghoshal, Alesya Evstratova, Daniel Trcka, Parisa Ghiasi, J. Javier Hernández, Jean Martin Beaulieu, Jeffrey L. Wrana, Liliana Attisano
Software Mentions: 6
Published: over 4 years ago

10.1155/2021/5545261

Ndufs1 Deficiency Aggravates the Mitochondrial Membrane Potential Dysfunction in Pressure Overload-Induced Myocardial Hypertrophy
Cited by: 17
Author(s): Rongjun Zou, Jun Tao, Junxiong Qiu, Wu Shi, Ming‐Hui Zou, Weidan Chen, Wenlei Li, Na Zhou, Shaoli Wang, Li Ma, Xinxin Chen
Software Mentions: 6
Published: over 3 years ago

10.1084/jem.20192386

Transcription cofactor GRIP1 differentially affects myeloid cell–driven neuroinflammation and response to IFN-β therapy
Cited by: 4
Author(s): Sanda Mimouna, David A. Rollins, Gayathri Shibu, Bowranigan Tharmalingam, Dinesh K Deochand, Xi Chen, David J. Oliver, Yurii Chinenov, Inez Rogatsky
Software Mentions: 6
Published: about 4 years ago

10.1084/jem.20200829

The mRNA m6A reader YTHDF2 suppresses proinflammatory pathways and sustains hematopoietic stem cell function
Cited by: 80
Author(s): Christopher Mapperley, Louie Van De Lagemaat, Hannah Lawson, Andrea Tavosanis, J Paris, Joana Campos, David Wotherspoon, Jozef Durko, Annika Sarapuu, Joong-Seon Choe, Ivayla Ivanova, Daniela Krause, Alex von Kriegsheim, Christian Much, Marcos Morgan, Richard I. Gregory, Adam J. Mead, Dónal O’Carroll, Kamil R. Kranc
Software Mentions: 6
Published: almost 4 years ago

10.1186/s12864-021-07469-6

WASP: a versatile, web-accessible single cell RNA-Seq processing platform
Cited by: 5
Author(s): Andreas Hoek, Katharina Maibach, Ebru Özmen, Ana Ivonne Vazquez‐Armendariz, Jan Philipp Mengel, Torsten Hain, Susanne Herold, Alexander Goesmann
Software Mentions: 6
Published: over 3 years ago

10.1186/s12864-021-07435-2

Blinatumomab-induced T cell activation at single cell transcriptome resolution
Cited by: 11
Author(s): Yi Huo, Zhonghua Sheng, Daniel Lu, Daniel C. Ellwanger, Chi-Ming Li, Oliver Homann, Songli Wang, Hong Mei Yin, Ruibao Ren
Software Mentions: 6
Published: over 3 years ago

10.1016/j.devcel.2018.06.028

Defining Lineage Potential and Fate Behavior of Precursors during Pancreas Development
Cited by: 36
Author(s): Magdalena K. Sznurkowska, Édouard Hannezo, Roberta Azzarelli, Steffen Rulands, Sonia Nestorowa, Christopher J. Hindley, Jennifer Nichols, Berthold Göttgens, Meritxell Huch, Anna Philpott, Benjamin D. Simons
Software Mentions: 6
Published: over 6 years ago

10.3389/fcell.2020.592348

Limited Mitochondrial Activity Coupled With Strong Expression of CD34, CD90 and EPCR Determines the Functional Fitness of ex vivo Expanded Human Hematopoietic Stem Cells
Cited by: 7
Author(s): Luena Papa, Mansour Djedaini, Tiphaine Martin, Mahtab Zangui, Kristin G. Beaumont, Robert Sebra, Ramon Parsons, Christoph Schaniel, Ronald Hoffman
Software Mentions: 5
Published: almost 4 years ago

10.1016/j.immuni.2019.05.002

Polychromic Reporter Mice Reveal Unappreciated Innate Lymphoid Cell Progenitor Heterogeneity and Elusive ILC3 Progenitors in Bone Marrow
Cited by: 85
Author(s): Jennifer Walker, Paula A. Clark, Alastair Crisp, Jillian L. Barlow, Aydan C H Szeto, Ana Carolina Franco Ferreira, Batika M. J. Rana, Helen E. Jolin, Noé Rodríguez-Rodríguez, Meera Sivasubramaniam, Richard Pannell, James Cruickshank, Maria Daly, Liora Haim-Vilmovsky, Sarah A. Teichmann, Andrew N. J. McKenzie
Software Mentions: 5
Published: over 5 years ago

10.7554/eLife.60225

RUNX1 marks a luminal castration-resistant lineage established at the onset of prostate development
Cited by: 28
Author(s): Renaud Mével, Ivana Steiner, Susan Mason, Laura C.A. Galbraith, Rahima Patel, Muhammad Zaki Hidayatullah Fadlullah, Imran Ahmad, Hing Y. Leung, Pedro Oliveira, Karen Blyth, Esther Baena, Georges Lacaud
Software Mentions: 5
Published: about 4 years ago

10.1007/s13238-020-00720-y

Integrative analysis of in vivo recording with single-cell RNA-seq data reveals molecular properties of light-sensitive neurons in mouse V1
Cited by: 9
Author(s): Jianwei Liu, Mengdi Wang, Le Sun, Na Pan, Changjiang Zhang, Junjing Zhang, Zhentao Zuo, Sheng He, Qian Wu, Xiaoqun Wang
Software Mentions: 5
Published: over 4 years ago

10.1186/s13059-019-1906-x

scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation
Cited by: 257
Author(s): Elo Madissoon, Anna Wilbrey-Clark, Ricardo J. Miragaia, Kourosh Saeb‐Parsy, Krishnaa Mahbubani, Nikitas Georgakopoulos, Philippa Harding, Krzysztof Polański, Ni Huang, Karol Nowicki-Osuch, Rebecca C. Fitzgerald, Kevin Loudon, John R. Ferdinand, Menna R. Clatworthy, Anthi Tsingene, Stijn van Dongen, Monika Dąbrowska, Minal Patel, Michael J T Stubbington, Sarah A. Teichmann, Oliver Stegle, Kerstin B. Meyer
Software Mentions: 5
Published: almost 5 years ago

10.1038/s41598-018-24725-0

Characterization of germ cell differentiation in the male mouse through single-cell RNA sequencing
Cited by: 68
Author(s): Söeren Lukassen, Elisabeth Bosch, Arif B. Ekici, Andreas Winterpacht
Software Mentions: 5
Published: over 6 years ago

10.3389/fonc.2021.557477

Unraveling Heterogeneity of Tumor Cells and Microenvironment and Its Clinical Implications for Triple Negative Breast Cancer
Cited by: 12
Author(s): Ke Jiang, Mengting Dong, Chunyang Li, Jiayu Sheng
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-020-76157-4

The bone marrow microenvironment of pre-B acute lymphoblastic leukemia at single-cell resolution
Cited by: 12
Author(s): Denise Anderson, Patrycja Skut, Anastasia M. Hughes, Emanuela Ferrari, Jennifer Tickner, Jiake Xu, Benjamin H. Mullin, Dave Tang, Sébastien Malinge, Ursula R. Kees, Rishi S. Kotecha, Timo Lassmann, Laurence C. Cheung
Software Mentions: 4
Published: about 4 years ago

10.1016/j.gpb.2018.08.003

VASC: Dimension Reduction and Visualization of Single-cell RNA-seq Data by Deep Variational Autoencoder
Cited by: 159
Author(s): Dongfang Wang, Jin Gu
Software Mentions: 4
Published: about 6 years ago

10.3389/fimmu.2020.00829

Treated HIV Infection Alters Phenotype but Not HIV-Specific Function of Peripheral Blood Natural Killer Cells
Cited by: 8
Author(s): Nancy Q. Zhao, Anne-Maud Ferreira, Philip Grant, Susan Holmes, Catherine A. Blish
Software Mentions: 4
Published: over 4 years ago

10.18632/oncotarget.27935

Controlling for cellular heterogeneity using single-cell deconvolution of gene expression reveals novel markers of colorectal tumors exhibiting microsatellite instability
Cited by: 5
Author(s): Matthew Devall, Graham Casey
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pgen.1007127

A novel prospective isolation of murine fetal liver progenitors to study in utero hematopoietic defects
Cited by: 7
Author(s): Julia Draper, Patrycja Sroczyńska, Muhammad Zaki Hidayatullah Fadlullah, Rahima Patel, Gillian Newton, Wolfgang Breitwieser, Valérie Kouskoff, Georges Lacaud
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-020-66848-3

Identification of cell types from single cell data using stable clustering
Cited by: 24
Author(s): Azam Peyvandipour, Adib Shafi, Nafiseh Saberian, Sorin Drăghici
Software Mentions: 4
Published: over 4 years ago

10.7554/eLife.30657

Wilms Tumor 1b defines a wound-specific sheath cell subpopulation associated with notochord repair
Cited by: 21
Author(s): Juan Carlos Lopez-Baez, Daniel J. Simpson, Laura Lleras Forero, Zhiqiang Zeng, Hannah Brunsdon, Angela Salzano, Alessandro Brombin, Cameron Wyatt, Witold M. Rybski, Leonie F. A. Huitema, Rodney M. Dale, Koichi Kawakami, Christoph Englert, Tamir Chandra, Stefan Schulte‐Merker, Nicholas D. Hastie, E. Elizabeth Patton
Software Mentions: 4
Published: over 6 years ago

10.7150/jca.49262

Pathologic evolution-related Gene Analysis based on both single-cell and bulk transcriptomics in Colorectal Cancer
Cited by: 3
Author(s): Jiali Li, Zhao-Yi Zeng, Jiarui Chen, Xingyu Liu, Xueping Jiang, Wenjie Sun, Yuan Luo, Jiangbo Ren, Yan Gong, Conghua Xie
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12967-020-02690-5

An analytical method for the identification of cell type-specific disease gene modules
Cited by: 5
Author(s): Jinting Guan, Yiping Lin, Yang Wang, Junchao Gao, Guoli Ji
Software Mentions: 3
Published: almost 4 years ago

10.1093/gigascience/giz144

A Galaxy-based training resource for single-cell RNA-sequencing quality control and analyses
Cited by: 4
Author(s): Graham Etherington, Nicola Soranzo, Suhaib Mohammed, Wilfried Haerty, Robert P. Davey, Federica Di Palma
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-021-88875-4

Synthetic single cell RNA sequencing data from small pilot studies using deep generative models
Cited by: 5
Author(s): Martin Treppner, Adrián Salas-Bastos, Moritz Hess, Stefan Lenz, Tanja Vogel, Harald Binder
Software Mentions: 3
Published: over 3 years ago

10.1242/dev.185595

Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain
Cited by: 45
Author(s): Christian Lange, Fabian Rost, Anja Machate, Susanne Reinhardt, Matthias Lesche, Anke Weber, Veronika Kuscha, Andreas Dahl, Steffen Rulands, Michael Brand
Software Mentions: 3
Published: almost 5 years ago

10.1186/s13059-019-1644-0

Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity
Cited by: 57
Author(s): Stephanie M. Linker, Lara Urban, Stephen J. Clark, Mariya Chhatriwala, Shradha Amatya, Davis J. McCarthy, Ingo Ebersberger, Ludovic Vallier, Wolf Reik, Oliver Stegle, Marc Jan Bonder
Software Mentions: 3
Published: over 5 years ago

10.3389/fphar.2021.657486

Caspase-11-Gasdermin D-Mediated Pyroptosis Is Involved in the Pathogenesis of Atherosclerosis
Cited by: 34
Author(s): Mengqing Jiang, Xuejing Sun, Suzhen Liu, Tao Yan, Yunming Shi, Yuanyuan Bai, Yujie Wang, Qiong Yang, Qize Yang, Weihong Jiang, Hong Yuan, Qixia Jiang, Jingjing Cai
Software Mentions: 3
Published: over 3 years ago

10.1093/molbev/msz290

Distinct Evolutionary Trajectories of Neuronal and Hair Cell Nicotinic Acetylcholine Receptors
Cited by: 26
Author(s): Irina Marcovich, Marcelo J. Moglie, Agustín Eduardo Carpaneto Freixas, Anabella Paola Trigila, Lucía F. Franchini, Paola V. Plazas, Marcela Lipovsek, Ana Belén Elgoyhen
Software Mentions: 3
Published: almost 5 years ago

10.1007/s00395-019-0765-7

Cell shape determines gene expression: cardiomyocyte morphotypic transcriptomes
Cited by: 11
Author(s): Payam Haftbaradaran Esfahani, Zaher Elbeck, Sven Sagasser, Xidan Li, Mohammad Bakhtiar Hossain, Husain Ahammad Talukdar, Rickard Sandberg, Ralph Knöll
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12944-021-01545-2

Negative correlation between endoglin levels and coronary atherosclerosis
Cited by: 2
Author(s): Haibin Chen, Yiping Wang, Bing Sun, Xiao Bao, Yu Tang, Feifei Huang, Sibo Zhu, Jiahong Xu
Software Mentions: 2
Published: about 3 years ago

10.1007/s00251-018-01099-1

The genomic organization and expression pattern of the low-affinity Fc gamma receptors (FcγR) in the Göttingen minipig
Cited by: 5
Author(s): Jérôme Egli, Roland Schmucki, Ben Loos, Stephan Reichl, Nils Grabole, Andreas Roller, Martin Ebeling, Alex Odermatt, Antonio Iglesias
Software Mentions: 2
Published: almost 6 years ago

Projects: bioconductor: scater

Papers Mentioning scater 79