bioconductor: baySeq | Projects | Ecosyste.ms: Papers

10.1186/s13059-016-0881-8

A survey of best practices for RNA-seq data analysis
Cited by: 1,691
Author(s): Ana Conesa, Pedro Madrigal, Sonia Tarazona, David Gomez-Cabrero, Alejandra Cervera, Andrew McPherson, Michał Wojciech Szcześniak, Daniel J. Gaffney, Laura L. Elo, Xuegong Zhang, A Mortazavi
Software Mentions: 21
Published: over 8 years ago

10.1186/s13059-014-0550-8

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Cited by: 49,504
Author(s): Michael I. Love, Wolfgang Huber, Simon Anders
Software Mentions: 16
Published: over 9 years ago

10.1371/journal.pone.0256196

Finding differentially expressed sRNA-Seq regions with srnadiff
Cited by: 2
Author(s): Matthias Zytnicki, Ignacio González
Software Mentions: 15
Published: over 2 years ago

10.1186/s12859-021-04193-6

Comparison study of differential abundance testing methods using two large Parkinson disease gut microbiome datasets derived from 16S amplicon sequencing
Cited by: 32
Author(s): Zachary D Wallen
Software Mentions: 14
Published: almost 3 years ago

10.1186/s12859-015-0794-7

Evaluation of methods for differential expression analysis on multi-group RNA-seq count data
Cited by: 47
Author(s): Min Tang, Jianqiang Sun, Kentaro Shimizu, Koji Kadota
Software Mentions: 13
Published: over 8 years ago

10.1186/s12859-016-1457-z

Empirical assessment of analysis workflows for differential expression analysis of human samples using RNA-Seq
Cited by: 55
Author(s): Claire Williams, Alyssa Baccarella, Jay Z. Parrish, Charles C. Kim
Software Mentions: 13
Published: over 7 years ago

10.1371/journal.pone.0190152

RNA-Seq differential expression analysis: An extended review and a software tool
Cited by: 389
Author(s): Juliana Costa-Silva, Douglas Silva Domingues, Fabrício Martins Lopes
Software Mentions: 12
Published: over 6 years ago

10.3390/ijms21010167

RNA-seq and ChIP-seq as Complementary Approaches for Comprehension of Plant Transcriptional Regulatory Mechanism
Cited by: 22
Author(s): Isiaka Ibrahim Muhammad, Sze Ling Kong, Siti Nor Akmar Abdullah, Umaiyal Munusamy
Software Mentions: 12
Published: over 4 years ago

10.3389/fonc.2020.584404

In silico Method in CRISPR/Cas System: An Expedite and Powerful Booster
Cited by: 6
Author(s): Yuwei Zhang, Guofang Zhao, Fatma Ahmed, Tianfei Yi, Shiyun Hu, Ting Cai, Qi Liao
Software Mentions: 11
Published: over 3 years ago

10.1186/s12859-016-1386-x

Robust differential expression analysis by learning discriminant boundary in multi-dimensional space of statistical attributes
Cited by: 0
Author(s): Yuanzhe Bei, Pengyu Hong
Software Mentions: 11
Published: over 7 years ago

10.1186/gb-2014-15-2-r29

voom: precision weights unlock linear model analysis tools for RNA-seq read counts
Cited by: 4,221
Author(s): Charity W. Law, Yunshun Chen, Wei Shi, Gordon K. Smyth
Software Mentions: 10
Published: over 10 years ago

10.1186/s13059-018-1466-5

Differential gene expression analysis tools exhibit substandard performance for long non-coding RNA-sequencing data
Cited by: 40
Author(s): Alemu Takele Assefa, Katrijn De Paepe, Celine Everaert, Pieter Mestdagh, Olivier Thas, Jo Vandesompele
Software Mentions: 10
Published: almost 6 years ago

10.1038/s41598-020-76881-x

Systematic comparison and assessment of RNA-seq procedures for gene expression quantitative analysis
Cited by: 81
Author(s): Luis A. Corchete, Elizabeta A. Rojas, Diego Alonso-López, Javier De Las Rivas, Norma C. Gutiérrez, F.J. Burguillo
Software Mentions: 10
Published: over 3 years ago

10.1186/s12575-018-0067-8

Silhouette Scores for Arbitrary Defined Groups in Gene Expression Data and Insights into Differential Expression Results
Cited by: 23
Author(s): Shitao Zhao, Jianqiang Sun, Kentaro Shimizu, Koji Kadota
Software Mentions: 10
Published: about 6 years ago

10.1186/s12859-017-1539-6

Model based heritability scores for high-throughput sequencing data
Cited by: 9
Author(s): Pratyaydipta Rudra, Wenmei Shi, Brian Vestal, Pamela Russell, Aaron Odell, Robin D. Dowell, Richard A. Radcliffe, Laura Saba, Katerina Kechris
Software Mentions: 10
Published: about 7 years ago

10.1186/s12859-017-1498-y

Evaluation of logistic regression models and effect of covariates for case–control study in RNA-Seq analysis
Cited by: 15
Author(s): Seung Hoan Choi, Adam Labadorf, Richard H. Myers, Kathryn L. Lunetta, Josée Dupuis, Anita L. DeStefano
Software Mentions: 10
Published: over 7 years ago

10.1186/s12864-015-1676-0

deGPS is a powerful tool for detecting differential expression in RNA-sequencing studies
Cited by: 14
Author(s): Chengcai Chu, Zhiming Fang, Xing Hua, Yaning Yang, Enguo Chen, Allen W. Cowley, Mingyu Liang, Pengyuan Liu, Yan Lu
Software Mentions: 9
Published: almost 9 years ago

10.3389/fpls.2020.01269

Analysis of Metabolites and Gene Expression Changes Relative to Apricot (Prunus armeniaca L.) Fruit Quality During Development and Ripening
Cited by: 27
Author(s): Beatriz Ester García-Gómez, David Ruiz, J. Salazar, M. Rubio, Pedro J. Martínez-García, Pedro Martínez‐Gómez
Software Mentions: 9
Published: almost 4 years ago

10.1186/1471-2164-16-S6-S3

RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application
Cited by: 54
Author(s): Mattia D’Antonio, Paolo D’Onorio De Meo, Matteo Pallocca, Ernesto Picardi, Anna Maria D’Erchia, Raffaele Calogero, Tiziana Castrignanò, Graziano Pesole
Software Mentions: 9
Published: almost 9 years ago

10.1186/s13059-015-0702-5

Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data
Cited by: 128
Author(s): Alexander Kanitz, Foivos Gypas, Andreas Gruber, Andreas Gruber, Georges Martín, Mihaela Zavolan
Software Mentions: 9
Published: almost 9 years ago

10.1186/1471-2164-16-S7-S14

Differential expression analysis of RNA sequencing data by incorporating non-exonic mapped reads
Cited by: 12
Author(s): Hung I Harry Chen, Yuanhang Liu, Yi Zou, Zhao Lai, Devanand Sarkar, Yufei Huang, Yidong Chen
Software Mentions: 9
Published: almost 9 years ago

10.3389/fcimb.2018.00326

In Search of Biomarkers for Pathogenesis and Control of Leishmaniasis by Global Analyses of Leishmania-Infected Macrophages
Cited by: 16
Author(s): Patrícia Sampaio Tavares Veras, Pablo Ivan Pereira Ramos, Juliana Perrone Bezerra de Menezes
Software Mentions: 8
Published: over 5 years ago

10.1186/1471-2105-14-219

TCC: an R package for comparing tag count data with robust normalization strategies
Cited by: 394
Author(s): Jianqiang Sun, Tomoaki Nishiyama, Kentaro Shimizu, Koji Kadota
Software Mentions: 8
Published: almost 11 years ago

10.1371/journal.pone.0031630

Optimizing a Massive Parallel Sequencing Workflow for Quantitative miRNA Expression Analysis
Cited by: 33
Author(s): Francesca Cordero, Marco Beccuti, Maddalena Arigoni, Susanna Donatelli, Raffaele Calogero
Software Mentions: 8
Published: about 12 years ago

10.1371/journal.pone.0125000

From Gigabyte to Kilobyte: A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data
Cited by: 6
Author(s): Jilong Li, Jie Hou, Sun Liang, Jordan Wilkins, Yuan Lu, Chad E. Niederhuth, Benjamin Ryan Merideth, Thomas P. Mawhinney, Valeri V. Mossine, C. Michael Greenlief, John C. Walker, William R. Folk, Mark Hannink, Dennis B. Lubahn, James A. Birchler, Jianlin Cheng
Software Mentions: 8
Published: about 9 years ago

10.1371/journal.pone.0232271

Benchmarking RNA-seq differential expression analysis methods using spike-in and simulation data
Cited by: 20
Author(s): Bukyung Baik, Susan A. Yoon, Dougu Nam
Software Mentions: 8
Published: about 4 years ago

10.1186/s12864-019-5926-4

lncDIFF: a novel quasi-likelihood method for differential expression analysis of non-coding RNA
Cited by: 6
Author(s): Qian Li, Xiaoqing Yu, Ritu Chaudhary, Robbert J.C. Slebos, Christine H. Chung, Xuefeng Wang
Software Mentions: 8
Published: almost 5 years ago

10.1186/s13059-020-02072-6

HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis
Cited by: 7
Author(s): Guy Karlebach, Peter J. Hansen, Diogo Veiga, Robin Steinhaus, Daniel Daniš, Sheng Li, Olga Anczuków, Peter N. Robinson
Software Mentions: 8
Published: almost 4 years ago

10.1186/s12864-016-2848-2

ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences
Cited by: 21
Author(s): Wentao Yang, Philip Rosenstiel, Hinrich Schulenburg
Software Mentions: 8
Published: almost 8 years ago

10.1186/gb-2013-14-9-r95

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data
Cited by: 594
Author(s): Franck Rapaport, Raya Khanin, Yupu Liang, Mono Pirun, Azra Krek, Paul Zumbo, Christopher E. Mason, Nicholas D. Socci, Doron Betel
Software Mentions: 8
Published: over 11 years ago

10.3389/fpls.2018.00108

Optimization of an RNA-Seq Differential Gene Expression Analysis Depending on Biological Replicate Number and Library Size
Cited by: 61
Author(s): Sophie Lamarre, Pierre Frasse, Mohamed Zouine, Delphine Labourdette, Elise Sainderichin, Guojian Hu, Véronique Le Berre-Anton, Mondher Bouzayen, Élie Maza
Software Mentions: 8
Published: over 6 years ago

10.3389/fgene.2018.00588

DREAMSeq: An Improved Method for Analyzing Differentially Expressed Genes in RNA-seq Data
Cited by: 10
Author(s): Zhihua Gao, Zhiyuan Zhao, Wenqiang Tang
Software Mentions: 8
Published: over 5 years ago

10.1155/2015/789516

Differential Expression Analysis in RNA-Seq by a Naive Bayes Classifier with Local Normalization
Cited by: 6
Author(s): Yongchao Dou, Xiaoli Guo, Lingling Yuan, David R. Holding, Chi Zhang
Software Mentions: 8
Published: over 9 years ago

10.1186/s40168-016-0208-8

Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies
Cited by: 124
Author(s): Jonathan Thorsen, Asker Brejnrod, Martin Steen Mortensen, Morten Arendt Rasmussen, Jakob Stokholm, Waleed Abu Al‐Soud, Søren J. Sørensen, Hans Bisgaard, Johannes Waage
Software Mentions: 8
Published: over 7 years ago

10.3390/e21030242

A Method Based on Differential Entropy-Like Function for Detecting Differentially Expressed Genes Across Multiple Conditions in RNA-Seq Studies
Cited by: 1
Author(s): Zhuo Wang, Shuilin Jin, Chiping Zhang
Software Mentions: 7
Published: about 5 years ago

10.1186/1471-2105-14-262

NPEBseq: nonparametric empirical bayesian-based procedure for differential expression analysis of RNA-seq data
Cited by: 30
Author(s): Yingtao Bi, Ramana V. Davuluri
Software Mentions: 7
Published: over 10 years ago

10.1371/journal.pone.0227760

A graph-based algorithm for RNA-seq data normalization
Cited by: 2
Author(s): Diem-Trang Tran, Aditya Bhaskara, Balagurunathan Kuberan, Matthew Might
Software Mentions: 7
Published: over 4 years ago

10.1186/1471-2105-14-91

A comparison of methods for differential expression analysis of RNA-seq data
Cited by: 725
Author(s): Charlotte Soneson, Mauro Delorenzi
Software Mentions: 7
Published: about 11 years ago

10.1093/bib/bbt086

Comparison of software packages for detecting differential expression in RNA-seq studies
Cited by: 317
Author(s): Fatemeh Seyednasrollah, Asta Laiho, Laura L. Elo
Software Mentions: 7
Published: over 10 years ago

10.3389/fgene.2012.00287

Bioinformatics of Cancer ncRNA in High Throughput Sequencing: Present State and Challenges
Cited by: 9
Author(s): Natasha Andressa Nogueira Jorge, Carlos Gil Ferreira, Fábio Passetti
Software Mentions: 7
Published: over 12 years ago

10.1186/s12864-018-4896-2

Refining a steroidogenic model: an analysis of RNA-seq datasets from insect prothoracic glands
Cited by: 8
Author(s): Panagiotis Moulos, Αλέξανδρος Αλεξανδράτος, Ioannis Nellas, Skarlatos G. Dedos
Software Mentions: 7
Published: almost 6 years ago

10.1371/journal.pone.0232646

Two-step mixed model approach to analyzing differential alternative RNA splicing
Cited by: 0
Author(s): Li Luo, Huining Kang, Xichen Li, Scott A. Ness, Christine A. Stidley
Software Mentions: 7
Published: over 3 years ago

10.1186/s12864-017-3938-5

A permutation-based non-parametric analysis of CRISPR screen data
Cited by: 26
Author(s): Gaoxiang Jia, Xinlei Wang, Guanghua Xiao
Software Mentions: 7
Published: almost 7 years ago

10.7717/peerj.8206

consensusDE: an R package for assessing consensus of multiple RNA-seq algorithms with RUV correction
Cited by: 24
Author(s): Ashley J. Waardenberg, Matthew A. Field
Software Mentions: 7
Published: over 4 years ago

10.1186/s12920-020-00808-8

Biomarker discovery in attention deficit hyperactivity disorder: RNA sequencing of whole blood in discordant twin and case-controlled cohorts
Cited by: 11
Author(s): Timothy A. McCaffrey, Georges St. Laurent, Dmitry Shtokalo, Денис Антонец, Yuri Vyatkin, Dan Jones, Eleanor Battison, Joel T. Nigg
Software Mentions: 7
Published: over 3 years ago

10.1038/srep35671

RNA sequencing analysis of human podocytes reveals glucocorticoid regulated gene networks targeting non-immune pathways
Cited by: 22
Author(s): Lulu Jiang, Charles Hindmarch, Mark F. Rogers, Colin Campbell, Christy Waterfall, Jane A. Coghill, Peter W. Mathieson, Gavin I. Welsh
Software Mentions: 6
Published: over 7 years ago

10.1038/s41598-019-41315-w

Novel Data Transformations for RNA-seq Differential Expression Analysis
Cited by: 23
Author(s): Zeyu Zhang, Danyang Yu, Minseok Seo, Craig P. Hersh, Scott T. Weiss, Weiliang Qiu
Software Mentions: 6
Published: about 5 years ago

10.1186/s12859-016-1208-1

NBLDA: negative binomial linear discriminant analysis for RNA-Seq data
Cited by: 34
Author(s): Kai Dong, Hongyu Zhao, Tiejun Tong, Xiang Wan
Software Mentions: 6
Published: over 7 years ago

10.1186/s12864-019-5686-1

aFold – using polynomial uncertainty modelling for differential gene expression estimation from RNA sequencing data
Cited by: 4
Author(s): Wentao Yang, Philip Rosenstiel, Hinrich Schulenburg
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pcbi.1005515

Mixture models reveal multiple positional bias types in RNA-Seq data and lead to accurate transcript concentration estimates
Cited by: 17
Author(s): Andreas Tuerk, Gregor Wiktorin, Serhat Güler
Software Mentions: 6
Published: about 7 years ago

10.1155/2015/178572

A Systematic Evaluation of Feature Selection and Classification Algorithms Using Simulated and Real miRNA Sequencing Data
Cited by: 7
Author(s): Sheng Yang, Li Guo, Fang Shao, Yang Zhao, Feng Chen
Software Mentions: 6
Published: over 9 years ago

10.1155/2013/203681

Time Series Expression Analyses Using RNA-seq: A Statistical Approach
Cited by: 23
Author(s): Sangwon Oh, Seongho Song, Gregory A. Grabowski, Hongyu Zhao, James P. Noonan
Software Mentions: 6
Published: over 11 years ago

10.1155/2014/248090

MultiRankSeq: Multiperspective Approach for RNAseq Differential Expression Analysis and Quality Control
Cited by: 49
Author(s): Yan Guo, Shilin Zhao, Fei Ye, Quanhu Sheng, Yu Shyr
Software Mentions: 6
Published: over 10 years ago

10.1371/journal.pgen.1005053

Phenotype Specific Analyses Reveal Distinct Regulatory Mechanism for Chronically Activated p53
Cited by: 47
Author(s): Kristina Kirschner, Shamith A. Samarajiwa, Jonathan Cairns, Suraj Menon, Pedro A. Pérez–Mancera, Kosuke Tomimatsu, Camino Bermejo‐Rodríguez, Yoko Itō, Tamir Chandra, Masako Narita, Scott K. Lyons, Andy G. Lynch, Hiroshi Kimurâ, Tetsuya Ohbayashi, Simon Tavaré
Software Mentions: 6
Published: about 9 years ago

10.3389/fncel.2019.00510

Brainstem-Evoked Transcription of Defensive Genes After Spinal Cord Injury
Cited by: 2
Author(s): Walter J. Jermakowicz, Melissa M. Carballosa-Gautam, Alberto Vitores, Ian D. Hentall
Software Mentions: 6
Published: over 4 years ago

10.1186/1471-2164-15-S10-S7

LFCseq: a nonparametric approach for differential expression analysis of RNA-seq data
Cited by: 16
Author(s): Bingqing Lin, Lifeng Zhang, Xin Chen
Software Mentions: 6
Published: over 9 years ago

10.1038/sdata.2016.73

Combinatory annotation of cell membrane receptors and signalling pathways of Bombyx mori prothoracic glands
Cited by: 7
Author(s): Panagiotis Moulos, Martina Samiotaki, George Panayotou, Skarlatos G. Dedos
Software Mentions: 6
Published: over 7 years ago

10.1186/s13059-015-0604-6

DGEclust: differential expression analysis of clustered count data
Cited by: 14
Author(s): Dimitrios V Vavoulis, Margherita Francescatto, Peter Heutink, Julian Gough
Software Mentions: 5
Published: about 9 years ago

10.1155/2013/481545

Stormbow: A Cloud-Based Tool for Reads Mapping and Expression Quantification in Large-Scale RNA-Seq Studies
Cited by: 13
Author(s): Shanrong Zhao, Kurt Prenger, Lance Smith
Software Mentions: 5
Published: over 10 years ago

10.1186/s12859-017-1780-z

Local sequence and sequencing depth dependent accuracy of RNA-seq reads
Cited by: 9
Author(s): Guoshuai Cai, Shoudan Liang, Xiaofeng Zheng, Feifei Xiao
Software Mentions: 5
Published: almost 7 years ago

10.1186/s13073-016-0348-2

Epigenomic and metabolic responses of hypothalamic POMC neurons to gestational nicotine exposure in adult offspring
Cited by: 9
Author(s): José P. Silva, Guerline Lambert, Derek Van Booven, Claes Wahlestedt
Software Mentions: 5
Published: over 7 years ago

10.1186/s13059-014-0527-7

The importance of study design for detecting differentially abundant features in high-throughput experiments
Cited by: 12
Author(s): Huaien Luo, Juntao Li, Burton Kuan Hui Chia, Paul Robson, Niranjan Nagarajan
Software Mentions: 5
Published: over 9 years ago

10.3389/fimmu.2020.558036

The Novel Omega-6 Fatty Acid Docosapentaenoic Acid Positively Modulates Brain Innate Immune Response for Resolving Neuroinflammation at Early and Late Stages of Humanized APOE-Based Alzheimer's Disease Models
Cited by: 14
Author(s): Qiu-Lan Ma, Cansheng Zhu, Marco Morselli, Trent Su, Matteo Pelligrini, Zhengqi Lu, Mychica Jones, Paul Denver, Daniel Castro, Xiaohong Gu, Frances Relampagos, Kaitlin Caoili, Bruce Teter, Sally A. Frautschy, Gregory M. Cole
Software Mentions: 5
Published: over 3 years ago

10.1093/bioinformatics/btz089

How well do RNA-Seq differential gene expression tools perform in a complex eukaryote? A case study in Arabidopsis thaliana
Cited by: 9
Author(s): Kimon Froussios, Nicholas J. Schurch, Katarzyna Mackinnon, Marek Gierliński, Céline Duc, Gordon G. Simpson, Geoffrey J. Barton
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-019-44962-1

The human tubal lavage proteome reveals biological processes that may govern the pathology of hydrosalpinx
Cited by: 8
Author(s): Elizabeth Yohannes, Avedis Kazanjian, Morgan E. Lindsay, Dennis T. Fujii, Nicholas Ieronimakis, Gregory E. Chow, Ronald D. Beesley, Ryan J. Heitmann, Richard O. Burney
Software Mentions: 5
Published: almost 5 years ago

10.1177/1177932219860817

Accurate Classification of Differential Expression Patterns in a Bayesian Framework With Robust Normalization for Multi-Group RNA-Seq Count Data
Cited by: 10
Author(s): Takayuki Osabe, Kentaro Shimizu, Koji Kadota
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0123658

A Powerful Statistical Approach for Large-Scale Differential Transcription Analysis
Cited by: 4
Author(s): Ying Tan, Anita M. Chandler, Arindam Chaudhury, Joel R. Neilson
Software Mentions: 5
Published: about 9 years ago

10.1371/journal.pone.0103207

A Comparative Study of Techniques for Differential Expression Analysis on RNA-Seq Data
Cited by: 195
Author(s): Zong Hong Zhang, Dhanisha J. Jhaveri, Vikki M. Marshall, Denis C. Bauer, Janette Edson, Ramesh Narayanan, Gregory J. Robinson, Andreas E. Lundberg, Perry F. Bartlett, Naomi R. Wray, Qiongyi Zhao
Software Mentions: 5
Published: almost 10 years ago

10.18632/oncotarget.9370

Practical aspects of NGS-based pathways analysis for personalized cancer science and medicine
Cited by: 13
Author(s): Ekaterina Kotelnikova, Mikhail A. Pyatnitskiy, A. G. Paleeva, O. S. Kremenetskaya, D. V. Vinogradov
Software Mentions: 4
Published: about 8 years ago

10.1186/1471-2105-15-81

spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data
Cited by: 89
Author(s): Kristoffer Vitting-Seerup, Bo T. Porse, Albin Sandelin, Johannes Waage
Software Mentions: 4
Published: about 10 years ago

10.1186/1471-2164-15-341

EXPRSS: an Illumina based high-throughput expression-profiling method to reveal transcriptional dynamics
Cited by: 34
Author(s): Ghanasyam Rallapalli, Eric Kemen, Alexandre Robert-Seilaniantz, Cécile Segonzac, Graham J. Etherington, Kee Hoon Sohn, Dan MacLean, Jonathan D. G. Jones
Software Mentions: 4
Published: about 10 years ago

10.1186/1471-2164-14-S8-S1

Interdisciplinary dialogue for education, collaboration, and innovation: Intelligent Biology and Medicine in and beyond 2013
Cited by: 49
Author(s): Bing Zhang, Yufei Huang, Jason McDermott, Rebecca H Posey, Hua Xu, Zhongming Zhao
Software Mentions: 4
Published: over 11 years ago

10.1186/1471-2164-14-S8-S2

Evaluation of read count based RNAseq analysis methods
Cited by: 50
Author(s): Yan Guo, Chung I. Li, Fei Ye, Yu Shyr
Software Mentions: 4
Published: over 11 years ago

10.1186/s12864-017-3809-0

Gene dispersion is the key determinant of the read count bias in differential expression analysis of RNA-seq data
Cited by: 20
Author(s): Susan A. Yoon, Dougu Nam
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12864-021-07409-4

Impact of PNPase on the transcriptome of Rhodobacter sphaeroides and its cooperation with RNase III and RNase E
Cited by: 7
Author(s): Daniel-Timon Spanka, Carina M. Reuscher, Gabriele Klug
Software Mentions: 4
Published: over 3 years ago

10.1186/1471-2164-15-S6-S18

Comparative exomics of Phalariscultivars under salt stress
Cited by: 12
Author(s): Niina Haiminen, Manfred Klaas, Zeyu Zhou, Filippo Utro, Paul Cormican, Thomas Didion, Christian S. Jensen, Christopher E. Mason, Susanne Barth, Laxmi Parida
Software Mentions: 4
Published: over 9 years ago

10.1186/s12918-018-0582-x

A powerful nonparametric method for detecting differentially co-expressed genes: distance correlation screening and edge-count test
Cited by: 6
Author(s): Qingyang Zhang
Software Mentions: 4
Published: about 6 years ago

10.1093/bioinformatics/btu274

Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation
Cited by: 64
Author(s): Tarmo Äijö, Vincent Butty, Zhi Chen, Verna Salo, Subhash Tripathi, Christopher B. Burge, Riitta Lahesmaa, Harri Lähdesmäki
Software Mentions: 4
Published: almost 10 years ago

10.1155/2015/862130

RNAseq by Total RNA Library Identifies Additional RNAs Compared to Poly(A) RNA Library
Cited by: 29
Author(s): Yan Guo, Shilin Zhao, Quanhu Sheng, Mingsheng Guo, Brian D. Lehmann, Jennifer A. Pietenpol, David C. Samuels, Yu Shyr
Software Mentions: 4
Published: over 9 years ago

10.1186/2049-2618-2-15

Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis
Cited by: 707
Author(s): Andrew D. Fernandes, Jennifer Reid, Jean M. Macklaim, T.A. McMurrough, David R. Edgell, Gregory B. Gloor
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.pone.0071462

Large Scale Comparison of Gene Expression Levels by Microarrays and RNAseq Using TCGA Data
Cited by: 163
Author(s): Yan Guo, Quanhu Sheng, Li Jiang, Fei Ye, David C. Samuels, Yu Shyr
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pone.0164766

RNA-Seq Count Data Modelling by Grey Relational Analysis and Nonparametric Gaussian Process
Cited by: 1
Author(s): Thanh Nguyen, Asim Bhatti, Samuel Yang, Saeid Nahavandi
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0190456

Mitochondrial DNA depletion by ethidium bromide decreases neuronal mitochondrial creatine kinase: Implications for striatal energy metabolism
Cited by: 18
Author(s): Emily B. Warren, Aidan Aicher, Joshua P. Fessel, Christine Konradi
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0115842

Identifying Glioblastoma Gene Networks Based on Hypergeometric Test Analysis
Cited by: 14
Author(s): Vasileios Stathias, Chiara Pastori, Tess Z. Griffin, Ricardo J. Komotar, Jennifer Clarke, Ming Zhang, Nagi G. Ayad
Software Mentions: 4
Published: over 9 years ago

10.1186/2045-3701-2-26

Statistical methods for identifying differentially expressed genes in RNA-Seq experiments
Cited by: 43
Author(s): Zhide Fang, Jeffrey A. Martin, Zhong Wang
Software Mentions: 4
Published: over 12 years ago

10.3389/fgene.2014.00035

The analytical landscape of static and temporal dynamics in transcriptome data
Cited by: 26
Author(s): Sangwon Oh, Seongho Song, Nupur Dasgupta, Gregory A. Grabowski
Software Mentions: 4
Published: over 10 years ago

10.3389/fgene.2014.00312

Gene expression responses of threespine stickleback to salinity: implications for salt-sensitive hypertension
Cited by: 33
Author(s): Gang Wang, Ence Yang, Kerri J. Smith, Yong Zeng, Guoli Ji, Richard E. Connon, Nann A. Fangue, James J. Cai
Software Mentions: 4
Published: over 9 years ago

10.3389/fmicb.2021.605095

Improvement of Free Fatty Acid Secretory Productivity in Aspergillus oryzae by Comprehensive Analysis on Time-Series Gene Expression
Cited by: 4
Author(s): Pui Shan Wong, Koichi Tamano, Sachiyo Aburatani
Software Mentions: 4
Published: about 3 years ago

10.3389/fpls.2016.01416

Comparative Analysis of miRNAs and Their Target Transcripts between a Spontaneous Late-Ripening Sweet Orange Mutant and Its Wild-Type Using Small RNA and Degradome Sequencing
Cited by: 19
Author(s): Juxun Wu, Saisai Zheng, Guizhi Feng, Hualin Yi
Software Mentions: 4
Published: over 7 years ago

10.1186/s13059-014-0554-4

MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens
Cited by: 1,433
Author(s): Wei Li, Xu Han, Tengfei Xiao, Le Cong, Michael I. Love, Feng Zhang, Rafael A. Irizarry, Jun S. Liu, Myles Brown, X Shirley Liu
Software Mentions: 4
Published: over 9 years ago

10.1186/1748-7188-7-5

A normalization strategy for comparing tag count data
Cited by: 72
Author(s): Koji Kadota, Tomoaki Nishiyama, Kentaro Shimizu
Software Mentions: 4
Published: about 12 years ago

10.1093/gbe/evv117

Variation in the X:Autosome Distribution of Male-Biased Genes amongDrosophila melanogasterTissues and Its Relationship with Dosage Compensation
Cited by: 28
Author(s): Ann Kathrin Huylmans, John Parsch
Software Mentions: 3
Published: almost 9 years ago

10.1534/g3.114.013417

Population- and Sex-Biased Gene Expression in the Excretion Organs of Drosophila melanogaster
Cited by: 34
Author(s): Ann Kathrin Huylmans, John Parsch
Software Mentions: 3
Published: over 9 years ago

10.1590/1678-4685-GMB-2016-0101

A comprehensive transcriptome analysis of skeletal muscles in two Polish pig breeds differing in fat and meat quality traits
Cited by: 32
Author(s): Katarzyna Piórkowska, Kacper Żukowski, Katarzyna Ropka‐Molik, M. Tyra, Artur Gurgul
Software Mentions: 3
Published: about 6 years ago

10.1186/1471-2164-14-171

Transcriptomics of morphological color change in polychromatic Midas cichlids
Cited by: 76
Author(s): Frederico Henning, Julia C. Jones, Paolo Franchini, Axel Meyer
Software Mentions: 3
Published: about 11 years ago

10.1186/1755-8794-6-S2-S1

Analysis of small-sample clinical genomics studies using multi-parameter shrinkage: application to high-throughput RNA interference screening
Cited by: 7
Author(s): Mark A. van de Wiel, Renée X. de Menezes, Ellen Siebring-van Olst, Victor W. van Beusechem
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pone.0070040

ABC Transporters in Dictyostelium discoideum Development
Cited by: 14
Author(s): Edward Roshan Miranda, Olga Zhuchenko, Marko Toplak, Balaji Santhanam, Blaž Zupan, Adam Kuspa, Gad Shaulsky
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0031526

The Transcriptome of Compatible and Incompatible Interactions of Potato (Solanum tuberosum) with Phytophthora infestans Revealed by DeepSAGE Analysis
Cited by: 55
Author(s): Gabor Gyetvai, Mads Sønderkær, Ulrike Göbel, Rico Basekow, Agim Ballvora, Maren Imhoff, Birgit Kersten, Kåre Lehmann Nielsen, Christiane Gebhardt
Software Mentions: 3
Published: over 12 years ago

10.1186/1471-2164-14-450

Transcriptomic and phylogenetic analysis of a bacterial cell cycle reveals strong associations between gene co-expression and evolution
Cited by: 49
Author(s): Gang Fang, Karla D. Passalacqua, Jason Hocking, Paula Montero Llopis, Mark Gerstein, Nicholas H. Bergman, Christine Jacobs‐Wagner
Software Mentions: 3
Published: almost 11 years ago

10.1186/1471-2164-16-S6-S2

FunPat: function-based pattern analysis on RNA-seq time series data
Cited by: 56
Author(s): Tiziana Sanavia, Francesca Finotello, Barbara Di Camillo
Software Mentions: 3
Published: almost 9 years ago

Projects: bioconductor: baySeq

Papers Mentioning baySeq 139