cran: PoissonSeq | 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/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: almost 9 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/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/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/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: about 6 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/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

10.1371/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: over 4 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

10.1186/s12864-018-5390-6

Stability of methods for differential expression analysis of RNA-seq data
Cited by: 14
Author(s): Bingqing Lin, Zhen Pang
Software Mentions: 7
Published: over 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: about 11 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: over 5 years ago

10.3390/jof7090700

Trends and Applications of Omics Technologies to Functional Characterisation of Enzymes and Protein Metabolites Produced by Fungi
Cited by: 3
Author(s): Grace N. Ijoma, Sylvie M Heri, Tonderayi Matambo, Memory Tekere
Software Mentions: 7
Published: about 3 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

10.1371/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: almost 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: almost 10 years ago

10.7717/peerj.576

Error estimates for the analysis of differential expression from RNA-seq count data
Cited by: 39
Author(s): Conrad J. Burden, Sumaira Qureshi, Susan R. Wilson
Software Mentions: 5
Published: almost 10 years ago

10.1186/s13059-015-0781-3

Do count-based differential expression methods perform poorly when genes are expressed in only one condition?
Cited by: 5
Author(s): Xiaobei Zhou, Mark D. Robinson
Software Mentions: 5
Published: almost 9 years ago

10.1371/journal.pone.0137782

Gene Ranking of RNA-Seq Data via Discriminant Non-Negative Matrix Factorization
Cited by: 23
Author(s): Zhilong Jia, Xiang Zhang, Naiyang Guan, Xiaochen Bo, Michael R. Barnes, Zhigang Luo
Software Mentions: 4
Published: about 9 years ago

10.1186/s12864-016-3219-8

Genome-wide gene expression and RNA half-life measurements allow predictions of regulation and metabolic behavior in Methanosarcina acetivorans
Cited by: 21
Author(s): J.R. Peterson, Sheng Shee Thor, Lars Köhler, Petra R. A. Kohler, William W. Metcalf, Zaida Luthey‐Schulten
Software Mentions: 4
Published: almost 8 years ago

10.1155/2015/621690

The Impact of Normalization Methods on RNA-Seq Data Analysis
Cited by: 81
Author(s): Joanna Zyprych-Walczak, Alicja Szabelska, Luiza Handschuh, Katarzyna Górczak, Kamila Klamecka, Marek Figlerowicz, Idzi Siatkowski
Software Mentions: 4
Published: over 9 years ago

10.1200/CCI.19.00118

Statistical Assessment of Depth Normalization for Small RNA Sequencing
Cited by: 7
Author(s): Li‐Xuan Qin, Jian Zou, Jiejun Shi, Ann Lee, Aleksandra Mihailović, Thalia A. Farazi, Thomas Tuschl, Samuel Singer
Software Mentions: 4
Published: almost 4 years ago

10.3389/fgene.2021.650795

SMIXnorm: Fast and Accurate RNA-Seq Data Normalization for Formalin-Fixed Paraffin-Embedded Samples
Cited by: 0
Author(s): Yin Shen, Xiaowei Zhan, Bo Yao, Guanghua Xiao, Xinlei Wang, Yang Xie
Software Mentions: 3
Published: over 3 years ago

10.1186/gb-2014-15-5-r71

A shared transcriptional program in early breast neoplasias despite genetic and clinical distinctions
Cited by: 28
Author(s): Alayne Brunner, Jun Li, Xiangqian Guo, Robert T. Sweeney, Sushama Varma, Shirley Zhu, Rui Li, Robert Tibshirani, Robert B. West
Software Mentions: 3
Published: over 10 years ago

10.1002/pld3.326

<i>slim shady</i> is a novel allele of <i>PHYTOCHROME B</i> present in the T‐DNA line SALK_015201
Cited by: 5
Author(s): Linkan Dash, Robert E. McEwan, Christian Montes, Ludvin Mejia, Justin W. Walley, Brian P. Dilkes, Dior R. Kelley
Software Mentions: 3
Published: over 3 years ago

10.1038/srep20957

A genome-wide search for epigenetically regulated genes in zebra finch using MethylCap-seq and RNA-seq
Cited by: 9
Author(s): Sandra Steyaert, Jolien Diddens, Jeroen Galle, Ellen De Meester, Sarah De Keulenaer, Antje Bakker, Nina Sohnius-Wilhelmi, Carolina Frankl-Vilches, Annemie Van der Linden, Wim Van Criekinge, Wim Vanden Berghe, Tim De Meyer
Software Mentions: 3
Published: over 8 years ago

10.1186/s13059-015-0782-2

Response to Zhou and Robinson
Cited by: 0
Author(s): Doron Betel, Nicholas D. Socci, Raya Khanin, Christopher E. Mason, Franck Rapaport
Software Mentions: 2
Published: almost 9 years ago

10.3390/ijms21228550

Multi-Omics Data Integration in Extracellular Vesicle Biology—Utopia or Future Reality?
Cited by: 24
Author(s): Leona Chiţoiu, Alexandra Dobranici, Mihaela Gherghiceanu, Sorina Dinescu, Marieta Costache
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12859-018-2382-0

Expression analysis of RNA sequencing data from human neural and glial cell lines depends on technical replication and normalization methods
Cited by: 3
Author(s): V. Bleu Knight, Elba E. Serrano
Software Mentions: 1
Published: almost 6 years ago

Ecosyste.ms: Papers

Projects: cran: PoissonSeq

Papers Mentioning PoissonSeq 30