Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: bioconductor: baySeq
https://packages.ecosyste.ms/registries/bioconductor.org/packages/baySeq
Empirical Bayesian analysis of patterns of differential expression in count data
1 version
Latest release: about 1 year ago
1 dependent package
115,922 downloads total
Papers Mentioning baySeq 139
10.1186/s13059-016-0881-8
A survey of best practices for RNA-seq data analysisCited 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: almost 9 years ago
10.1186/s13059-014-0550-8
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2Cited by: 49,504
Author(s): Michael I. Love, Wolfgang Huber, Simon Anders
Software Mentions: 16
Published: about 10 years ago
10.1371/journal.pone.0256196
Finding differentially expressed sRNA-Seq regions with srnadiffCited by: 2
Author(s): Matthias Zytnicki, Ignacio González
Software Mentions: 15
Published: over 3 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 sequencingCited by: 32
Author(s): Zachary D Wallen
Software Mentions: 14
Published: over 3 years ago
10.1186/s12859-015-0794-7
Evaluation of methods for differential expression analysis on multi-group RNA-seq count dataCited by: 47
Author(s): Min Tang, Jianqiang Sun, Kentaro Shimizu, Koji Kadota
Software Mentions: 13
Published: about 9 years ago
10.1186/s12859-016-1457-z
Empirical assessment of analysis workflows for differential expression analysis of human samples using RNA-SeqCited by: 55
Author(s): Claire Williams, Alyssa Baccarella, Jay Z. Parrish, Charles C. Kim
Software Mentions: 13
Published: almost 8 years ago
10.1371/journal.pone.0190152
RNA-Seq differential expression analysis: An extended review and a software toolCited by: 389
Author(s): Juliana Costa-Silva, Douglas Silva Domingues, Fabrício Martins Lopes
Software Mentions: 12
Published: about 7 years ago
10.3390/ijms21010167
RNA-seq and ChIP-seq as Complementary Approaches for Comprehension of Plant Transcriptional Regulatory MechanismCited by: 22
Author(s): Isiaka Ibrahim Muhammad, Sze Ling Kong, Siti Nor Akmar Abdullah, Umaiyal Munusamy
Software Mentions: 12
Published: almost 5 years ago
10.3389/fonc.2020.584404
In silico Method in CRISPR/Cas System: An Expedite and Powerful BoosterCited by: 6
Author(s): Yuwei Zhang, Guofang Zhao, Fatma Ahmed, Tianfei Yi, Shiyun Hu, Ting Cai, Qi Liao
Software Mentions: 11
Published: about 4 years ago
10.1186/s12859-016-1386-x
Robust differential expression analysis by learning discriminant boundary in multi-dimensional space of statistical attributesCited by: 0
Author(s): Yuanzhe Bei, Pengyu Hong
Software Mentions: 11
Published: about 8 years ago
10.1186/gb-2014-15-2-r29
voom: precision weights unlock linear model analysis tools for RNA-seq read countsCited by: 4,221
Author(s): Charity W. Law, Yunshun Chen, Wei Shi, Gordon K. Smyth
Software Mentions: 10
Published: almost 11 years ago
10.1186/s13059-018-1466-5
Differential gene expression analysis tools exhibit substandard performance for long non-coding RNA-sequencing dataCited by: 40
Author(s): Alemu Takele Assefa, Katrijn De Paepe, Celine Everaert, Pieter Mestdagh, Olivier Thas, Jo Vandesompele
Software Mentions: 10
Published: over 6 years ago
10.1038/s41598-020-76881-x
Systematic comparison and assessment of RNA-seq procedures for gene expression quantitative analysisCited 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: about 4 years ago
10.1186/s12575-018-0067-8
Silhouette Scores for Arbitrary Defined Groups in Gene Expression Data and Insights into Differential Expression ResultsCited by: 23
Author(s): Shitao Zhao, Jianqiang Sun, Kentaro Shimizu, Koji Kadota
Software Mentions: 10
Published: almost 7 years ago
10.1186/s12859-017-1539-6
Model based heritability scores for high-throughput sequencing dataCited 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: almost 8 years ago
10.1186/s12859-017-1498-y
Evaluation of logistic regression models and effect of covariates for case–control study in RNA-Seq analysisCited by: 15
Author(s): Seung Hoan Choi, Adam Labadorf, Richard H. Myers, Kathryn L. Lunetta, Josée Dupuis, Anita L. DeStefano
Software Mentions: 10
Published: almost 8 years ago
10.1186/s12864-015-1676-0
deGPS is a powerful tool for detecting differential expression in RNA-sequencing studiesCited 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: over 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 RipeningCited 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: over 4 years ago
10.1186/1471-2164-16-S6-S3
RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web applicationCited 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: over 9 years ago
10.1186/s13059-015-0702-5
Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq dataCited by: 128
Author(s): Alexander Kanitz, Foivos Gypas, Andreas Gruber, Andreas Gruber, Georges Martín, Mihaela Zavolan
Software Mentions: 9
Published: over 9 years ago
10.1186/1471-2164-16-S7-S14
Differential expression analysis of RNA sequencing data by incorporating non-exonic mapped readsCited by: 12
Author(s): Hung I Harry Chen, Yuanhang Liu, Yi Zou, Zhao Lai, Devanand Sarkar, Yufei Huang, Yidong Chen
Software Mentions: 9
Published: over 9 years ago
10.3389/fcimb.2018.00326
In Search of Biomarkers for Pathogenesis and Control of Leishmaniasis by Global Analyses of Leishmania-Infected MacrophagesCited by: 16
Author(s): Patrícia Sampaio Tavares Veras, Pablo Ivan Pereira Ramos, Juliana Perrone Bezerra de Menezes
Software Mentions: 8
Published: over 6 years ago
10.1186/1471-2105-14-219
TCC: an R package for comparing tag count data with robust normalization strategiesCited by: 394
Author(s): Jianqiang Sun, Tomoaki Nishiyama, Kentaro Shimizu, Koji Kadota
Software Mentions: 8
Published: over 11 years ago
10.1371/journal.pone.0031630
Optimizing a Massive Parallel Sequencing Workflow for Quantitative miRNA Expression AnalysisCited by: 33
Author(s): Francesca Cordero, Marco Beccuti, Maddalena Arigoni, Susanna Donatelli, Raffaele Calogero
Software Mentions: 8
Published: almost 13 years ago
10.1371/journal.pone.0125000
From Gigabyte to Kilobyte: A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics DataCited 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: over 9 years ago
10.1371/journal.pone.0232271
Benchmarking RNA-seq differential expression analysis methods using spike-in and simulation dataCited by: 20
Author(s): Bukyung Baik, Susan A. Yoon, Dougu Nam
Software Mentions: 8
Published: over 4 years ago
10.1186/s12864-019-5926-4
lncDIFF: a novel quasi-likelihood method for differential expression analysis of non-coding RNACited by: 6
Author(s): Qian Li, Xiaoqing Yu, Ritu Chaudhary, Robbert J.C. Slebos, Christine H. Chung, Xuefeng Wang
Software Mentions: 8
Published: over 5 years ago
10.1186/s13059-020-02072-6
HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysisCited 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: over 4 years ago
10.1186/s12864-016-2848-2
ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differencesCited by: 21
Author(s): Wentao Yang, Philip Rosenstiel, Hinrich Schulenburg
Software Mentions: 8
Published: over 8 years ago
10.1186/gb-2013-14-9-r95
Comprehensive evaluation of differential gene expression analysis methods for RNA-seq dataCited 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: almost 12 years ago
10.3389/fpls.2018.00108
Optimization of an RNA-Seq Differential Gene Expression Analysis Depending on Biological Replicate Number and Library SizeCited 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: almost 7 years ago
10.3389/fgene.2018.00588
DREAMSeq: An Improved Method for Analyzing Differentially Expressed Genes in RNA-seq DataCited by: 10
Author(s): Zhihua Gao, Zhiyuan Zhao, Wenqiang Tang
Software Mentions: 8
Published: about 6 years ago
10.1155/2015/789516
Differential Expression Analysis in RNA-Seq by a Naive Bayes Classifier with Local NormalizationCited by: 6
Author(s): Yongchao Dou, Xiaoli Guo, Lingling Yuan, David R. Holding, Chi Zhang
Software Mentions: 8
Published: almost 10 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 studiesCited 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: about 8 years ago
10.3390/e21030242
A Method Based on Differential Entropy-Like Function for Detecting Differentially Expressed Genes Across Multiple Conditions in RNA-Seq StudiesCited by: 1
Author(s): Zhuo Wang, Shuilin Jin, Chiping Zhang
Software Mentions: 7
Published: almost 6 years ago
10.1186/1471-2105-14-262
NPEBseq: nonparametric empirical bayesian-based procedure for differential expression analysis of RNA-seq dataCited by: 30
Author(s): Yingtao Bi, Ramana V. Davuluri
Software Mentions: 7
Published: over 11 years ago
10.1371/journal.pone.0227760
A graph-based algorithm for RNA-seq data normalizationCited by: 2
Author(s): Diem-Trang Tran, Aditya Bhaskara, Balagurunathan Kuberan, Matthew Might
Software Mentions: 7
Published: almost 5 years ago
10.1186/1471-2105-14-91
A comparison of methods for differential expression analysis of RNA-seq dataCited by: 725
Author(s): Charlotte Soneson, Mauro Delorenzi
Software Mentions: 7
Published: almost 12 years ago
10.1093/bib/bbt086
Comparison of software packages for detecting differential expression in RNA-seq studiesCited by: 317
Author(s): Fatemeh Seyednasrollah, Asta Laiho, Laura L. Elo
Software Mentions: 7
Published: about 11 years ago
10.3389/fgene.2012.00287
Bioinformatics of Cancer ncRNA in High Throughput Sequencing: Present State and ChallengesCited by: 9
Author(s): Natasha Andressa Nogueira Jorge, Carlos Gil Ferreira, Fábio Passetti
Software Mentions: 7
Published: almost 13 years ago
10.1186/s12864-018-4896-2
Refining a steroidogenic model: an analysis of RNA-seq datasets from insect prothoracic glandsCited by: 8
Author(s): Panagiotis Moulos, Αλέξανδρος Αλεξανδράτος, Ioannis Nellas, Skarlatos G. Dedos
Software Mentions: 7
Published: over 6 years ago
10.1371/journal.pone.0232646
Two-step mixed model approach to analyzing differential alternative RNA splicingCited by: 0
Author(s): Li Luo, Huining Kang, Xichen Li, Scott A. Ness, Christine A. Stidley
Software Mentions: 7
Published: about 4 years ago
10.1186/s12864-017-3938-5
A permutation-based non-parametric analysis of CRISPR screen dataCited by: 26
Author(s): Gaoxiang Jia, Xinlei Wang, Guanghua Xiao
Software Mentions: 7
Published: over 7 years ago
10.7717/peerj.8206
consensusDE: an R package for assessing consensus of multiple RNA-seq algorithms with RUV correctionCited by: 24
Author(s): Ashley J. Waardenberg, Matthew A. Field
Software Mentions: 7
Published: about 5 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 cohortsCited 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: about 4 years ago
10.1038/srep35671
RNA sequencing analysis of human podocytes reveals glucocorticoid regulated gene networks targeting non-immune pathwaysCited 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: about 8 years ago
10.1038/s41598-019-41315-w
Novel Data Transformations for RNA-seq Differential Expression AnalysisCited by: 23
Author(s): Zeyu Zhang, Danyang Yu, Minseok Seo, Craig P. Hersh, Scott T. Weiss, Weiliang Qiu
Software Mentions: 6
Published: almost 6 years ago
10.1186/s12859-016-1208-1
NBLDA: negative binomial linear discriminant analysis for RNA-Seq dataCited by: 34
Author(s): Kai Dong, Hongyu Zhao, Tiejun Tong, Xiang Wan
Software Mentions: 6
Published: over 8 years ago
10.1186/s12864-019-5686-1
aFold – using polynomial uncertainty modelling for differential gene expression estimation from RNA sequencing dataCited by: 4
Author(s): Wentao Yang, Philip Rosenstiel, Hinrich Schulenburg
Software Mentions: 6
Published: over 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 estimatesCited by: 17
Author(s): Andreas Tuerk, Gregor Wiktorin, Serhat Güler
Software Mentions: 6
Published: over 7 years ago
10.1155/2015/178572
A Systematic Evaluation of Feature Selection and Classification Algorithms Using Simulated and Real miRNA Sequencing DataCited by: 7
Author(s): Sheng Yang, Li Guo, Fang Shao, Yang Zhao, Feng Chen
Software Mentions: 6
Published: almost 10 years ago
10.1155/2013/203681
Time Series Expression Analyses Using RNA-seq: A Statistical ApproachCited by: 23
Author(s): Sangwon Oh, Seongho Song, Gregory A. Grabowski, Hongyu Zhao, James P. Noonan
Software Mentions: 6
Published: almost 12 years ago
10.1155/2014/248090
MultiRankSeq: Multiperspective Approach for RNAseq Differential Expression Analysis and Quality ControlCited by: 49
Author(s): Yan Guo, Shilin Zhao, Fei Ye, Quanhu Sheng, Yu Shyr
Software Mentions: 6
Published: almost 11 years ago
10.1371/journal.pgen.1005053
Phenotype Specific Analyses Reveal Distinct Regulatory Mechanism for Chronically Activated p53Cited 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: almost 10 years ago
10.3389/fncel.2019.00510
Brainstem-Evoked Transcription of Defensive Genes After Spinal Cord InjuryCited by: 2
Author(s): Walter J. Jermakowicz, Melissa M. Carballosa-Gautam, Alberto Vitores, Ian D. Hentall
Software Mentions: 6
Published: about 5 years ago
10.1186/1471-2164-15-S10-S7
LFCseq: a nonparametric approach for differential expression analysis of RNA-seq dataCited by: 16
Author(s): Bingqing Lin, Lifeng Zhang, Xin Chen
Software Mentions: 6
Published: about 10 years ago
10.1038/sdata.2016.73
Combinatory annotation of cell membrane receptors and signalling pathways of Bombyx mori prothoracic glandsCited by: 7
Author(s): Panagiotis Moulos, Martina Samiotaki, George Panayotou, Skarlatos G. Dedos
Software Mentions: 6
Published: over 8 years ago
10.1186/s13059-015-0604-6
DGEclust: differential expression analysis of clustered count dataCited by: 14
Author(s): Dimitrios V Vavoulis, Margherita Francescatto, Peter Heutink, Julian Gough
Software Mentions: 5
Published: almost 10 years ago
10.1155/2013/481545
Stormbow: A Cloud-Based Tool for Reads Mapping and Expression Quantification in Large-Scale RNA-Seq StudiesCited by: 13
Author(s): Shanrong Zhao, Kurt Prenger, Lance Smith
Software Mentions: 5
Published: over 11 years ago
10.1186/s12859-017-1780-z
Local sequence and sequencing depth dependent accuracy of RNA-seq readsCited by: 9
Author(s): Guoshuai Cai, Shoudan Liang, Xiaofeng Zheng, Feifei Xiao
Software Mentions: 5
Published: over 7 years ago
10.1186/s13073-016-0348-2
Epigenomic and metabolic responses of hypothalamic POMC neurons to gestational nicotine exposure in adult offspringCited by: 9
Author(s): José P. Silva, Guerline Lambert, Derek Van Booven, Claes Wahlestedt
Software Mentions: 5
Published: over 8 years ago
10.1186/s13059-014-0527-7
The importance of study design for detecting differentially abundant features in high-throughput experimentsCited by: 12
Author(s): Huaien Luo, Juntao Li, Burton Kuan Hui Chia, Paul Robson, Niranjan Nagarajan
Software Mentions: 5
Published: about 10 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 ModelsCited 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: about 4 years ago
10.1093/bioinformatics/btz089
How well do RNA-Seq differential gene expression tools perform in a complex eukaryote? A case study in <i>Arabidopsis thaliana</i>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: almost 6 years ago
10.1038/s41598-019-44962-1
The human tubal lavage proteome reveals biological processes that may govern the pathology of hydrosalpinxCited 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: over 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 DataCited by: 10
Author(s): Takayuki Osabe, Kentaro Shimizu, Koji Kadota
Software Mentions: 5
Published: almost 6 years ago
10.1371/journal.pone.0123658
A Powerful Statistical Approach for Large-Scale Differential Transcription AnalysisCited by: 4
Author(s): Ying Tan, Anita M. Chandler, Arindam Chaudhury, Joel R. Neilson
Software Mentions: 5
Published: over 9 years ago
10.1371/journal.pone.0103207
A Comparative Study of Techniques for Differential Expression Analysis on RNA-Seq DataCited 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: over 10 years ago
10.18632/oncotarget.9370
Practical aspects of NGS-based pathways analysis for personalized cancer science and medicineCited by: 13
Author(s): Ekaterina Kotelnikova, Mikhail A. Pyatnitskiy, A. G. Paleeva, O. S. Kremenetskaya, D. V. Vinogradov
Software Mentions: 4
Published: over 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 dataCited by: 89
Author(s): Kristoffer Vitting-Seerup, Bo T. Porse, Albin Sandelin, Johannes Waage
Software Mentions: 4
Published: almost 11 years ago
10.1186/1471-2164-15-341
EXPRSS: an Illumina based high-throughput expression-profiling method to reveal transcriptional dynamicsCited 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: over 10 years ago
10.1186/1471-2164-14-S8-S1
Interdisciplinary dialogue for education, collaboration, and innovation: Intelligent Biology and Medicine in and beyond 2013Cited by: 49
Author(s): Bing Zhang, Yufei Huang, Jason McDermott, Rebecca H Posey, Hua Xu, Zhongming Zhao
Software Mentions: 4
Published: almost 12 years ago
10.1186/1471-2164-14-S8-S2
Evaluation of read count based RNAseq analysis methodsCited by: 50
Author(s): Yan Guo, Chung I. Li, Fei Ye, Yu Shyr
Software Mentions: 4
Published: almost 12 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 dataCited by: 20
Author(s): Susan A. Yoon, Dougu Nam
Software Mentions: 4
Published: over 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 ECited by: 7
Author(s): Daniel-Timon Spanka, Carina M. Reuscher, Gabriele Klug
Software Mentions: 4
Published: almost 4 years ago
10.1186/1471-2164-15-S6-S18
Comparative exomics of Phalariscultivars under salt stressCited 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: about 10 years ago
10.1186/s12918-018-0582-x
A powerful nonparametric method for detecting differentially co-expressed genes: distance correlation screening and edge-count testCited by: 6
Author(s): Qingyang Zhang
Software Mentions: 4
Published: over 6 years ago
10.1093/bioinformatics/btu274
Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiationCited 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: over 10 years ago
10.1155/2015/862130
RNAseq by Total RNA Library Identifies Additional RNAs Compared to Poly(A) RNA LibraryCited 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: almost 10 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 analysisCited 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: over 10 years ago
10.1371/journal.pone.0071462
Large Scale Comparison of Gene Expression Levels by Microarrays and RNAseq Using TCGA DataCited by: 163
Author(s): Yan Guo, Quanhu Sheng, Li Jiang, Fei Ye, David C. Samuels, Yu Shyr
Software Mentions: 4
Published: over 11 years ago
10.1371/journal.pone.0164766
RNA-Seq Count Data Modelling by Grey Relational Analysis and Nonparametric Gaussian ProcessCited by: 1
Author(s): Thanh Nguyen, Asim Bhatti, Samuel Yang, Saeid Nahavandi
Software Mentions: 4
Published: about 8 years ago
10.1371/journal.pone.0190456
Mitochondrial DNA depletion by ethidium bromide decreases neuronal mitochondrial creatine kinase: Implications for striatal energy metabolismCited by: 18
Author(s): Emily B. Warren, Aidan Aicher, Joshua P. Fessel, Christine Konradi
Software Mentions: 4
Published: almost 7 years ago
10.1371/journal.pone.0115842
Identifying Glioblastoma Gene Networks Based on Hypergeometric Test AnalysisCited 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: almost 10 years ago
10.1186/2045-3701-2-26
Statistical methods for identifying differentially expressed genes in RNA-Seq experimentsCited by: 43
Author(s): Zhide Fang, Jeffrey A. Martin, Zhong Wang
Software Mentions: 4
Published: almost 13 years ago
10.3389/fgene.2014.00035
The analytical landscape of static and temporal dynamics in transcriptome dataCited by: 26
Author(s): Sangwon Oh, Seongho Song, Nupur Dasgupta, Gregory A. Grabowski
Software Mentions: 4
Published: almost 11 years ago
10.3389/fgene.2014.00312
Gene expression responses of threespine stickleback to salinity: implications for salt-sensitive hypertensionCited 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 10 years ago
10.3389/fmicb.2021.605095
Improvement of Free Fatty Acid Secretory Productivity in Aspergillus oryzae by Comprehensive Analysis on Time-Series Gene ExpressionCited by: 4
Author(s): Pui Shan Wong, Koichi Tamano, Sachiyo Aburatani
Software Mentions: 4
Published: over 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 SequencingCited by: 19
Author(s): Juxun Wu, Saisai Zheng, Guizhi Feng, Hualin Yi
Software Mentions: 4
Published: over 8 years ago
10.1186/s13059-014-0554-4
MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screensCited 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: about 10 years ago
10.1186/1748-7188-7-5
A normalization strategy for comparing tag count dataCited by: 72
Author(s): Koji Kadota, Tomoaki Nishiyama, Kentaro Shimizu
Software Mentions: 4
Published: over 12 years ago
10.1093/gbe/evv117
Variation in the X:Autosome Distribution of Male-Biased Genes among<i>Drosophila melanogaster</i>Tissues and Its Relationship with Dosage CompensationCited by: 28
Author(s): Ann Kathrin Huylmans, John Parsch
Software Mentions: 3
Published: over 9 years ago
10.1534/g3.114.013417
Population- and Sex-Biased Gene Expression in the Excretion Organs of <i>Drosophila melanogaster</i>Cited by: 34
Author(s): Ann Kathrin Huylmans, John Parsch
Software Mentions: 3
Published: about 10 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 traitsCited by: 32
Author(s): Katarzyna Piórkowska, Kacper Żukowski, Katarzyna Ropka‐Molik, M. Tyra, Artur Gurgul
Software Mentions: 3
Published: almost 7 years ago
10.1186/1471-2164-14-171
Transcriptomics of morphological color change in polychromatic Midas cichlidsCited by: 76
Author(s): Frederico Henning, Julia C. Jones, Paolo Franchini, Axel Meyer
Software Mentions: 3
Published: almost 12 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 screeningCited 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: almost 12 years ago
10.1371/journal.pone.0070040
ABC Transporters in Dictyostelium discoideum DevelopmentCited by: 14
Author(s): Edward Roshan Miranda, Olga Zhuchenko, Marko Toplak, Balaji Santhanam, Blaž Zupan, Adam Kuspa, Gad Shaulsky
Software Mentions: 3
Published: over 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 AnalysisCited 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: almost 13 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 evolutionCited 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: over 11 years ago
10.1186/1471-2164-16-S6-S2
FunPat: function-based pattern analysis on RNA-seq time series dataCited by: 56
Author(s): Tiziana Sanavia, Francesca Finotello, Barbara Di Camillo
Software Mentions: 3
Published: over 9 years ago