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List of co-cited articles
71 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity



Current best practices in single-cell RNA-seq analysis: a tutorial.
Malte D Luecken, Fabian J Theis. Mol Syst Biol 2019
346
50

Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R.
Davis J McCarthy, Kieran R Campbell, Aaron T L Lun, Quin F Wills. Bioinformatics 2017
423
42

Massively parallel digital transcriptional profiling of single cells.
Grace X Y Zheng, Jessica M Terry, Phillip Belgrader, Paul Ryvkin, Zachary W Bent, Ryan Wilson, Solongo B Ziraldo, Tobias D Wheeler, Geoff P McDermott, Junjie Zhu,[...]. Nat Commun 2017
42

Comprehensive Integration of Single-Cell Data.
Tim Stuart, Andrew Butler, Paul Hoffman, Christoph Hafemeister, Efthymia Papalexi, William M Mauck, Yuhan Hao, Marlon Stoeckius, Peter Smibert, Rahul Satija. Cell 2019
35

Orchestrating single-cell analysis with Bioconductor.
Robert A Amezquita, Aaron T L Lun, Etienne Becht, Vince J Carey, Lindsay N Carpp, Ludwig Geistlinger, Federico Marini, Kevin Rue-Albrecht, Davide Risso, Charlotte Soneson,[...]. Nat Methods 2020
90
35


Performance Assessment and Selection of Normalization Procedures for Single-Cell RNA-Seq.
Michael B Cole, Davide Risso, Allon Wagner, David DeTomaso, John Ngai, Elizabeth Purdom, Sandrine Dudoit, Nir Yosef. Cell Syst 2019
43
28

A comparison of automatic cell identification methods for single-cell RNA sequencing data.
Tamim Abdelaal, Lieke Michielsen, Davy Cats, Dylan Hoogduin, Hailiang Mei, Marcel J T Reinders, Ahmed Mahfouz. Genome Biol 2019
105
28

Exponential scaling of single-cell RNA-seq in the past decade.
Valentine Svensson, Roser Vento-Tormo, Sarah A Teichmann. Nat Protoc 2018
270
28

Benchmarking single-cell RNA-sequencing protocols for cell atlas projects.
Elisabetta Mereu, Atefeh Lafzi, Catia Moutinho, Christoph Ziegenhain, Davis J McCarthy, Adrián Álvarez-Varela, Eduard Batlle, Sagar, Dominic Grün, Julia K Lau,[...]. Nat Biotechnol 2020
87
28


The Human Cell Atlas.
Aviv Regev, Sarah A Teichmann, Eric S Lander, Ido Amit, Christophe Benoist, Ewan Birney, Bernd Bodenmiller, Peter Campbell, Piero Carninci, Menna Clatworthy,[...]. Elife 2017
710
28

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database.
Luke Zappia, Belinda Phipson, Alicia Oshlack. PLoS Comput Biol 2018
91
21

Benchmarking single cell RNA-sequencing analysis pipelines using mixture control experiments.
Luyi Tian, Xueyi Dong, Saskia Freytag, Kim-Anh Lê Cao, Shian Su, Abolfazl JalalAbadi, Daniela Amann-Zalcenstein, Tom S Weber, Azadeh Seidi, Jafar S Jabbari,[...]. Nat Methods 2019
89
21

Challenges in unsupervised clustering of single-cell RNA-seq data.
Vladimir Yu Kiselev, Tallulah S Andrews, Martin Hemberg. Nat Rev Genet 2019
234
21

Eleven grand challenges in single-cell data science.
David Lähnemann, Johannes Köster, Ewa Szczurek, Davis J McCarthy, Stephanie C Hicks, Mark D Robinson, Catalina A Vallejos, Kieran R Campbell, Niko Beerenwinkel, Ahmed Mahfouz,[...]. Genome Biol 2020
171
21

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
21

A comparison of single-cell trajectory inference methods.
Wouter Saelens, Robrecht Cannoodt, Helena Todorov, Yvan Saeys. Nat Biotechnol 2019
319
21

Computational and analytical challenges in single-cell transcriptomics.
Oliver Stegle, Sarah A Teichmann, John C Marioni. Nat Rev Genet 2015
548
21

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
21

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
21


Alevin efficiently estimates accurate gene abundances from dscRNA-seq data.
Avi Srivastava, Laraib Malik, Tom Smith, Ian Sudbery, Rob Patro. Genome Biol 2019
52
21

Low Bias Local Intrinsic Dimension Estimation from Expected Simplex Skewness.
Kerstin Johnsson, Charlotte Soneson, Magnus Fontes. IEEE Trans Pattern Anal Mach Intell 2015
6
50

PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data.
Oscar Franzén, Li-Ming Gan, Johan L M Björkegren. Database (Oxford) 2019
152
14

Classification of low quality cells from single-cell RNA-seq data.
Tomislav Ilicic, Jong Kyoung Kim, Aleksandra A Kolodziejczyk, Frederik Otzen Bagger, Davis James McCarthy, John C Marioni, Sarah A Teichmann. Genome Biol 2016
231
14

The human mitochondrial transcriptome.
Tim R Mercer, Shane Neph, Marcel E Dinger, Joanna Crawford, Martin A Smith, Anne-Marie J Shearwood, Eric Haugen, Cameron P Bracken, Oliver Rackham, John A Stamatoyannopoulos,[...]. Cell 2011
465
14

KEGG: kyoto encyclopedia of genes and genomes.
M Kanehisa, S Goto. Nucleic Acids Res 2000
14

MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data.
Greg Finak, Andrew McDavid, Masanao Yajima, Jingyuan Deng, Vivian Gersuk, Alex K Shalek, Chloe K Slichter, Hannah W Miller, M Juliana McElrath, Martin Prlic,[...]. Genome Biol 2015
654
14

Single-cell RNA sequencing technologies and bioinformatics pipelines.
Byungjin Hwang, Ji Hyun Lee, Duhee Bang. Exp Mol Med 2018
403
14

Single-cell RNA sequencing of adult mouse testes.
Soeren Lukassen, Elisabeth Bosch, Arif B Ekici, Andreas Winterpacht. Sci Data 2018
18
14

An Introduction to the Analysis of Single-Cell RNA-Sequencing Data.
Aisha A AlJanahi, Mark Danielsen, Cynthia E Dunbar. Mol Ther Methods Clin Dev 2018
47
14

Spatial reconstruction of single-cell gene expression data.
Rahul Satija, Jeffrey A Farrell, David Gennert, Alexander F Schier, Aviv Regev. Nat Biotechnol 2015
14

A curated database reveals trends in single-cell transcriptomics.
Valentine Svensson, Eduardo da Veiga Beltrame, Lior Pachter. Database (Oxford) 2020
27
14

Limitations of alignment-free tools in total RNA-seq quantification.
Douglas C Wu, Jun Yao, Kevin S Ho, Alan M Lambowitz, Claus O Wilke. BMC Genomics 2018
29
14

A systematic evaluation of single cell RNA-seq analysis pipelines.
Beate Vieth, Swati Parekh, Christoph Ziegenhain, Wolfgang Enard, Ines Hellmann. Nat Commun 2019
89
14


SCDC: bulk gene expression deconvolution by multiple single-cell RNA sequencing references.
Meichen Dong, Aatish Thennavan, Eugene Urrutia, Yun Li, Charles M Perou, Fei Zou, Yuchao Jiang. Brief Bioinform 2021
26
14


mRNA-Seq whole-transcriptome analysis of a single cell.
Fuchou Tang, Catalin Barbacioru, Yangzhou Wang, Ellen Nordman, Clarence Lee, Nanlan Xu, Xiaohui Wang, John Bodeau, Brian B Tuch, Asim Siddiqui,[...]. Nat Methods 2009
14

A systematic performance evaluation of clustering methods for single-cell RNA-seq data.
Angelo Duò, Mark D Robinson, Charlotte Soneson. F1000Res 2018
93
14

Putative cell type discovery from single-cell gene expression data.
Zhichao Miao, Pablo Moreno, Ni Huang, Irene Papatheodorou, Alvis Brazma, Sarah A Teichmann. Nat Methods 2020
21
14

SCENIC: single-cell regulatory network inference and clustering.
Sara Aibar, Carmen Bravo González-Blas, Thomas Moerman, Vân Anh Huynh-Thu, Hana Imrichova, Gert Hulselmans, Florian Rambow, Jean-Christophe Marine, Pierre Geurts, Jan Aerts,[...]. Nat Methods 2017
698
14

Inferring pathway activity toward precise disease classification.
Eunjung Lee, Han-Yu Chuang, Jong-Won Kim, Trey Ideker, Doheon Lee. PLoS Comput Biol 2008
292
14

Mapping the Mouse Cell Atlas by Microwell-Seq.
Xiaoping Han, Renying Wang, Yincong Zhou, Lijiang Fei, Huiyu Sun, Shujing Lai, Assieh Saadatpour, Ziming Zhou, Haide Chen, Fang Ye,[...]. Cell 2018
433
14

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
Aravind Subramanian, Pablo Tamayo, Vamsi K Mootha, Sayan Mukherjee, Benjamin L Ebert, Michael A Gillette, Amanda Paulovich, Scott L Pomeroy, Todd R Golub, Eric S Lander,[...]. Proc Natl Acad Sci U S A 2005
14

SciBet as a portable and fast single cell type identifier.
Chenwei Li, Baolin Liu, Boxi Kang, Zedao Liu, Yedan Liu, Changya Chen, Xianwen Ren, Zemin Zhang. Nat Commun 2020
14
14

GSVA: gene set variation analysis for microarray and RNA-seq data.
Sonja Hänzelmann, Robert Castelo, Justin Guinney. BMC Bioinformatics 2013
14

Detection and removal of barcode swapping in single-cell RNA-seq data.
Jonathan A Griffiths, Arianne C Richard, Karsten Bach, Aaron T L Lun, John C Marioni. Nat Commun 2018
69
14


Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.