Zhong Wang, Mark Gerstein, Michael Snyder. Nat Rev Genet 2009
Times Cited: 6574
Times Cited: 6574
Times Cited
Times Co-cited
Similarity
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
20
Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
14
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
13
The Sequence Alignment/Map format and SAMtools.
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin. Bioinformatics 2009
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin. Bioinformatics 2009
12
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.
Bo Li, Colin N Dewey. BMC Bioinformatics 2011
Bo Li, Colin N Dewey. BMC Bioinformatics 2011
11
HISAT: a fast spliced aligner with low memory requirements.
Daehwan Kim, Ben Langmead, Steven L Salzberg. Nat Methods 2015
Daehwan Kim, Ben Langmead, Steven L Salzberg. Nat Methods 2015
9
STAR: ultrafast universal RNA-seq aligner.
Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras. Bioinformatics 2013
Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras. Bioinformatics 2013
9
Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.
K J Livak, T D Schmittgen. Methods 2001
K J Livak, T D Schmittgen. Methods 2001
8
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features.
Yang Liao, Gordon K Smyth, Wei Shi. Bioinformatics 2014
Yang Liao, Gordon K Smyth, Wei Shi. Bioinformatics 2014
8
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads.
Mihaela Pertea, Geo M Pertea, Corina M Antonescu, Tsung-Cheng Chang, Joshua T Mendell, Steven L Salzberg. Nat Biotechnol 2015
Mihaela Pertea, Geo M Pertea, Corina M Antonescu, Tsung-Cheng Chang, Joshua T Mendell, Steven L Salzberg. Nat Biotechnol 2015
8
7
limma powers differential expression analyses for RNA-sequencing and microarray studies.
Matthew E Ritchie, Belinda Phipson, Di Wu, Yifang Hu, Charity W Law, Wei Shi, Gordon K Smyth. Nucleic Acids Res 2015
Matthew E Ritchie, Belinda Phipson, Di Wu, Yifang Hu, Charity W Law, Wei Shi, Gordon K Smyth. Nucleic Acids Res 2015
7
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
M Ashburner, C A Ball, J A Blake, D Botstein, H Butler, J M Cherry, A P Davis, K Dolinski, S S Dwight, J T Eppig,[...]. Nat Genet 2000
M Ashburner, C A Ball, J A Blake, D Botstein, H Butler, J M Cherry, A P Davis, K Dolinski, S S Dwight, J T Eppig,[...]. Nat Genet 2000
7
6
Mapping and quantifying mammalian transcriptomes by RNA-Seq.
Ali Mortazavi, Brian A Williams, Kenneth McCue, Lorian Schaeffer, Barbara Wold. Nat Methods 2008
Ali Mortazavi, Brian A Williams, Kenneth McCue, Lorian Schaeffer, Barbara Wold. Nat Methods 2008
6
Near-optimal probabilistic RNA-seq quantification.
Nicolas L Bray, Harold Pimentel, Páll Melsted, Lior Pachter. Nat Biotechnol 2016
Nicolas L Bray, Harold Pimentel, Páll Melsted, Lior Pachter. Nat Biotechnol 2016
6
5
Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Paul Shannon, Andrew Markiel, Owen Ozier, Nitin S Baliga, Jonathan T Wang, Daniel Ramage, Nada Amin, Benno Schwikowski, Trey Ideker. Genome Res 2003
Paul Shannon, Andrew Markiel, Owen Ozier, Nitin S Baliga, Jonathan T Wang, Daniel Ramage, Nada Amin, Benno Schwikowski, Trey Ideker. Genome Res 2003
5
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
Fuchou Tang, Catalin Barbacioru, Yangzhou Wang, Ellen Nordman, Clarence Lee, Nanlan Xu, Xiaohui Wang, John Bodeau, Brian B Tuch, Asim Siddiqui,[...]. Nat Methods 2009
5
A survey of best practices for RNA-seq data analysis.
Ana Conesa, Pedro Madrigal, Sonia Tarazona, David Gomez-Cabrero, Alejandra Cervera, Andrew McPherson, Michał Wojciech Szcześniak, Daniel J Gaffney, Laura L Elo, Xuegong Zhang,[...]. Genome Biol 2016
Ana Conesa, Pedro Madrigal, Sonia Tarazona, David Gomez-Cabrero, Alejandra Cervera, Andrew McPherson, Michał Wojciech Szcześniak, Daniel J Gaffney, Laura L Elo, Xuegong Zhang,[...]. Genome Biol 2016
5
Salmon provides fast and bias-aware quantification of transcript expression.
Rob Patro, Geet Duggal, Michael I Love, Rafael A Irizarry, Carl Kingsford. Nat Methods 2017
Rob Patro, Geet Duggal, Michael I Love, Rafael A Irizarry, Carl Kingsford. Nat Methods 2017
5
clusterProfiler: an R package for comparing biological themes among gene clusters.
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. OMICS 2012
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. OMICS 2012
5
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
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
5
Full-length transcriptome assembly from RNA-Seq data without a reference genome.
Manfred G Grabherr, Brian J Haas, Moran Yassour, Joshua Z Levin, Dawn A Thompson, Ido Amit, Xian Adiconis, Lin Fan, Raktima Raychowdhury, Qiandong Zeng,[...]. Nat Biotechnol 2011
Manfred G Grabherr, Brian J Haas, Moran Yassour, Joshua Z Levin, Dawn A Thompson, Ido Amit, Xian Adiconis, Lin Fan, Raktima Raychowdhury, Qiandong Zeng,[...]. Nat Biotechnol 2011
5
HTSeq--a Python framework to work with high-throughput sequencing data.
Simon Anders, Paul Theodor Pyl, Wolfgang Huber. Bioinformatics 2015
Simon Anders, Paul Theodor Pyl, Wolfgang Huber. Bioinformatics 2015
5
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.
Brian J Haas, Alexie Papanicolaou, Moran Yassour, Manfred Grabherr, Philip D Blood, Joshua Bowden, Matthew Brian Couger, David Eccles, Bo Li, Matthias Lieber,[...]. Nat Protoc 2013
Brian J Haas, Alexie Papanicolaou, Moran Yassour, Manfred Grabherr, Philip D Blood, Joshua Bowden, Matthew Brian Couger, David Eccles, Bo Li, Matthias Lieber,[...]. Nat Protoc 2013
5
RNA sequencing: advances, challenges and opportunities.
Fatih Ozsolak, Patrice M Milos. Nat Rev Genet 2011
Fatih Ozsolak, Patrice M Milos. Nat Rev Genet 2011
5
TopHat: discovering splice junctions with RNA-Seq.
Cole Trapnell, Lior Pachter, Steven L Salzberg. Bioinformatics 2009
Cole Trapnell, Lior Pachter, Steven L Salzberg. Bioinformatics 2009
4
BEDTools: a flexible suite of utilities for comparing genomic features.
Aaron R Quinlan, Ira M Hall. Bioinformatics 2010
Aaron R Quinlan, Ira M Hall. Bioinformatics 2010
4
Comparison of RNA-Seq and microarray in transcriptome profiling of activated T cells.
Shanrong Zhao, Wai-Ping Fung-Leung, Anton Bittner, Karen Ngo, Xuejun Liu. PLoS One 2014
Shanrong Zhao, Wai-Ping Fung-Leung, Anton Bittner, Karen Ngo, Xuejun Liu. PLoS One 2014
4
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.
Felipe A Simão, Robert M Waterhouse, Panagiotis Ioannidis, Evgenia V Kriventseva, Evgeny M Zdobnov. Bioinformatics 2015
Felipe A Simão, Robert M Waterhouse, Panagiotis Ioannidis, Evgenia V Kriventseva, Evgeny M Zdobnov. Bioinformatics 2015
4
SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads.
Yinlong Xie, Gengxiong Wu, Jingbo Tang, Ruibang Luo, Jordan Patterson, Shanlin Liu, Weihua Huang, Guangzhu He, Shengchang Gu, Shengkang Li,[...]. Bioinformatics 2014
Yinlong Xie, Gengxiong Wu, Jingbo Tang, Ruibang Luo, Jordan Patterson, Shanlin Liu, Weihua Huang, Guangzhu He, Shengchang Gu, Shengkang Li,[...]. Bioinformatics 2014
4
voom: Precision weights unlock linear model analysis tools for RNA-seq read counts.
Charity W Law, Yunshun Chen, Wei Shi, Gordon K Smyth. Genome Biol 2014
Charity W Law, Yunshun Chen, Wei Shi, Gordon K Smyth. Genome Biol 2014
4
The transcriptional landscape of the yeast genome defined by RNA sequencing.
Ugrappa Nagalakshmi, Zhong Wang, Karl Waern, Chong Shou, Debasish Raha, Mark Gerstein, Michael Snyder. Science 2008
Ugrappa Nagalakshmi, Zhong Wang, Karl Waern, Chong Shou, Debasish Raha, Mark Gerstein, Michael Snyder. Science 2008
4
A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors.
Donald M Bryant, Kimberly Johnson, Tia DiTommaso, Timothy Tickle, Matthew Brian Couger, Duygu Payzin-Dogru, Tae J Lee, Nicholas D Leigh, Tzu-Hsing Kuo, Francis G Davis,[...]. Cell Rep 2017
Donald M Bryant, Kimberly Johnson, Tia DiTommaso, Timothy Tickle, Matthew Brian Couger, Duygu Payzin-Dogru, Tae J Lee, Nicholas D Leigh, Tzu-Hsing Kuo, Francis G Davis,[...]. Cell Rep 2017
4
Gene ontology analysis for RNA-seq: accounting for selection bias.
Matthew D Young, Matthew J Wakefield, Gordon K Smyth, Alicia Oshlack. Genome Biol 2010
Matthew D Young, Matthew J Wakefield, Gordon K Smyth, Alicia Oshlack. Genome Biol 2010
4
MultiQC: summarize analysis results for multiple tools and samples in a single report.
Philip Ewels, Måns Magnusson, Sverker Lundin, Max Käller. Bioinformatics 2016
Philip Ewels, Måns Magnusson, Sverker Lundin, Max Käller. Bioinformatics 2016
4
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.
Cole Trapnell, Brian A Williams, Geo Pertea, Ali Mortazavi, Gordon Kwan, Marijke J van Baren, Steven L Salzberg, Barbara J Wold, Lior Pachter. Nat Biotechnol 2010
Cole Trapnell, Brian A Williams, Geo Pertea, Ali Mortazavi, Gordon Kwan, Marijke J van Baren, Steven L Salzberg, Barbara J Wold, Lior Pachter. Nat Biotechnol 2010
4
A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity.
Martin Jinek, Krzysztof Chylinski, Ines Fonfara, Michael Hauer, Jennifer A Doudna, Emmanuelle Charpentier. Science 2012
Martin Jinek, Krzysztof Chylinski, Ines Fonfara, Michael Hauer, Jennifer A Doudna, Emmanuelle Charpentier. Science 2012
3
KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases.
Chen Xie, Xizeng Mao, Jiaju Huang, Yang Ding, Jianmin Wu, Shan Dong, Lei Kong, Ge Gao, Chuan-Yun Li, Liping Wei. Nucleic Acids Res 2011
Chen Xie, Xizeng Mao, Jiaju Huang, Yang Ding, Jianmin Wu, Shan Dong, Lei Kong, Ge Gao, Chuan-Yun Li, Liping Wei. Nucleic Acids Res 2011
3
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.
Cole Trapnell, Adam Roberts, Loyal Goff, Geo Pertea, Daehwan Kim, David R Kelley, Harold Pimentel, Steven L Salzberg, John L Rinn, Lior Pachter. Nat Protoc 2012
Cole Trapnell, Adam Roberts, Loyal Goff, Geo Pertea, Daehwan Kim, David R Kelley, Harold Pimentel, Steven L Salzberg, John L Rinn, Lior Pachter. Nat Protoc 2012
3
Spatial reconstruction of single-cell gene expression data.
Rahul Satija, Jeffrey A Farrell, David Gennert, Alexander F Schier, Aviv Regev. Nat Biotechnol 2015
Rahul Satija, Jeffrey A Farrell, David Gennert, Alexander F Schier, Aviv Regev. Nat Biotechnol 2015
3
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
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
3
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences.
Weizhong Li, Adam Godzik. Bioinformatics 2006
Weizhong Li, Adam Godzik. Bioinformatics 2006
3
Bridger: a new framework for de novo transcriptome assembly using RNA-seq data.
Zheng Chang, Guojun Li, Juntao Liu, Yu Zhang, Cody Ashby, Deli Liu, Carole L Cramer, Xiuzhen Huang. Genome Biol 2015
Zheng Chang, Guojun Li, Juntao Liu, Yu Zhang, Cody Ashby, Deli Liu, Carole L Cramer, Xiuzhen Huang. Genome Biol 2015
3
Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling.
Nicholas T Ingolia, Sina Ghaemmaghami, John R S Newman, Jonathan S Weissman. Science 2009
Nicholas T Ingolia, Sina Ghaemmaghami, John R S Newman, Jonathan S Weissman. Science 2009
3
The Cancer Genome Atlas Pan-Cancer analysis project.
John N Weinstein, Eric A Collisson, Gordon B Mills, Kenna R Mills Shaw, Brad A Ozenberger, Kyle Ellrott, Ilya Shmulevich, Chris Sander, Joshua M Stuart. Nat Genet 2013
John N Weinstein, Eric A Collisson, Gordon B Mills, Kenna R Mills Shaw, Brad A Ozenberger, Kyle Ellrott, Ilya Shmulevich, Chris Sander, Joshua M Stuart. Nat Genet 2013
3
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.