cran: NBPSeq | Projects | Ecosyste.ms: Papers

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: almost 8 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: 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 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: almost 8 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: over 9 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: almost 6 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: almost 10 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: over 11 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: over 6 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: over 11 years ago

10.1186/s12859-015-0664-3

Confident difference criterion: a new Bayesian differentially expressed gene selection algorithm with applications
Cited by: 5
Author(s): Fang Yu, Ming Hui Chen, Lynn Kuo, Heather Talbott, John S. Davis
Software Mentions: 6
Published: over 9 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: almost 11 years ago

10.1534/g3.116.027045

Differential Expression of Genes Involved in Host Recognition, Attachment, and Degradation in the Mycoparasite <i>Tolypocladium ophioglossoides</i>
Cited by: 20
Author(s): C. Alisha Quandt, Yanming Di, Justin Elser, Pankaj Jaiswal, Joseph W. Spatafora
Software Mentions: 6
Published: over 8 years ago

10.1371/journal.pone.0025279

GENE-Counter: A Computational Pipeline for the Analysis of RNA-Seq Data for Gene Expression Differences
Cited by: 62
Author(s): Jason S. Cumbie, Jeffrey A. Kimbrel, Yanming Di, Daniel W. Schafer, Larry J. Wilhelm, Samuel E. Fox, Christopher Sullivan, Aron D. Curzon, James C. Carrington, Todd C. Mockler, Jeff H. Chang
Software Mentions: 6
Published: about 13 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: about 8 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: over 10 years ago

10.1371/journal.pone.0159182

LPEseq: Local-Pooled-Error Test for RNA Sequencing Experiments with a Small Number of Replicates
Cited by: 6
Author(s): Jungsoo Gim, Sungho Won, Taesung Park
Software Mentions: 5
Published: over 8 years ago

10.3390/cells9091924

Microcurrent Stimulation Triggers MAPK Signaling and TGF-β1 Release in Fibroblast and Osteoblast-Like Cell Lines
Cited by: 14
Author(s): Evangelia Konstantinou, Zoi Zagoriti, Anastasia Pyriochou, Konstantinos Poulas
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0120117

The Level of Residual Dispersion Variation and the Power of Differential Expression Tests for RNA-Seq Data
Cited by: 1
Author(s): Gu Mi, Yanming Di
Software Mentions: 5
Published: over 9 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: almost 12 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: over 12 years ago

10.1371/journal.pone.0119254

Goodness-of-Fit Tests and Model Diagnostics for Negative Binomial Regression of RNA Sequencing Data
Cited by: 12
Author(s): Gu Mi, Yanming Di, Daniel W. Schafer
Software Mentions: 4
Published: over 9 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: almost 12 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: almost 10 years ago

10.1186/1471-2164-13-484

Efficient experimental design and analysis strategies for the detection of differential expression using RNA-Sequencing
Cited by: 180
Author(s): José A Robles, Sumaira Qureshi, Stuart Stephen, Susan R. Wilson, Conrad J. Burden, Jennifer Taylor
Software Mentions: 3
Published: about 12 years ago

10.1371/journal.pone.0046128

Length Bias Correction in Gene Ontology Enrichment Analysis Using Logistic Regression
Cited by: 30
Author(s): Gu Mi, Yanming Di, Sarah C. Emerson, Jason S. Cumbie, Jeff H. Chang
Software Mentions: 3
Published: about 12 years ago

10.1186/s12864-015-1461-0

GRACOMICS: software for graphical comparison of multiple results with omics data
Cited by: 7
Author(s): Minseok Seo, Joon Yoon, Taesung Park
Software Mentions: 3
Published: over 9 years ago

10.1038/s41598-018-21146-x

Circulating miRNAs as diagnostic biomarkers for adolescent idiopathic scoliosis
Cited by: 27
Author(s): José Luis García-Giménez, Pedro Antonio Rubio-Belmar, Lorena Peiró-Chova, David Hervás, Daymé González-Rodríguez, José Santiago Ibáñez-Cabellos, Paloma Bas-Hermida, Salvador Mena-Mollá, Eva García-López, Federico V. Pallardó, Teresa Bas
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12864-015-1666-2

RNA-Seq analysis of resistant and susceptible potato varieties during the early stages of potato virus Y infection
Cited by: 56
Author(s): Aymeric Goyer, Launa L. Hamlin, J. M. Crosslin, Alex Buchanan, Jeff H. Chang
Software Mentions: 2
Published: over 9 years ago

10.7717/peerj.2791

Identifying stably expressed genes from multiple RNA-Seq data sets
Cited by: 12
Author(s): Bin Zhuo, Sarah C. Emerson, Jeff H. Chang, Yanming Di
Software Mentions: 2
Published: almost 8 years ago

10.3389/fmed.2021.705071

Joint Modeling of RNAseq and Radiomics Data for Glioma Molecular Characterization and Prediction
Cited by: 3
Author(s): Zeina A. Shboul, Norou Diawara, Arastoo Vossough, James Y. Chen, Khan M. Iftekharuddin
Software Mentions: 2
Published: over 3 years ago

10.3390/genes2040689

RNA-Seq for Plant Pathogenic Bacteria
Cited by: 8
Author(s): Jeffrey A. Kimbrel, Yanming Di, Jason S. Cumbie, Jeff H. Chang
Software Mentions: 2
Published: about 13 years ago

10.7717/peerj.5199

Searching for best lower dimensional visualization angles for high dimensional RNA-Seq data
Cited by: 0
Author(s): Wanli Zhang, Yanming Di
Software Mentions: 1
Published: over 6 years ago

Ecosyste.ms: Papers

Projects: cran: NBPSeq

Papers Mentioning NBPSeq 32