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: cran: QuasiSeq

https://packages.ecosyste.ms/registries/cran.r-project.org/packages/QuasiSeq

Analyzing RNA Sequencing Count Tables Using Quasi-Likelihood
11 versions
Latest release: over 2 years ago
303 downloads last month

Papers Mentioning QuasiSeq 22

From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline
Cited by: 415
Author(s): Yunshun Chen, Aaron T. L. Lun, Gordon K. Smyth
Software Mentions: 15
Published: over 8 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: over 6 years ago

10.1186/s12859-016-0994-9

Sample size calculation while controlling false discovery rate for differential expression analysis with RNA-sequencing experiments
Cited by: 79
Author(s): Ran Bi, Peng Liu
Software Mentions: 9
Published: over 8 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: over 5 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: almost 7 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

10.7717/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: about 10 years ago

10.1371/journal.pone.0081415

Dispersion Estimation and Its Effect on Test Performance in RNA-seq Data Analysis: A Simulation-Based Comparison of Methods
Cited by: 29
Author(s): Will Landau, Peng Liu
Software Mentions: 5
Published: almost 11 years ago

10.3389/fgene.2018.00441

Gene Co-expression Analysis Indicates Potential Pathways and Regulators of Beef Tenderness in Nellore Cattle
Cited by: 30
Author(s): Tassia M. Goncalves, Luciana Correia de Almeida Regitano, James E. Koltes, Aline Silva Mello Cesar, Sónia Cristina da Silva Andrade, Gérson Barreto Mourão, G. Gasparin, Gabriel Costa Monteiro Moreira, Eric R. Fritz-Waters, James M. Reecy
Software Mentions: 5
Published: about 6 years ago

10.1186/s13059-017-1328-6

Substantial contribution of genetic variation in the expression of transcription factors to phenotypic variation revealed by eRD-GWAS
Cited by: 49
Author(s): Hung‐Ying Lin, Qiang Liu, Li Xiao, Jinliang Yang, Sanzhen Liu, Yinlian Huang, Michael J. Scanlon, Dan Nettleton, Patrick S. Schnable
Software Mentions: 4
Published: about 7 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

10.1371/journal.pone.0136765

In-Depth Duodenal Transcriptome Survey in Chickens with Divergent Feed Efficiency Using RNA-Seq
Cited by: 35
Author(s): Guoqiang Yi, Jiahui Yuan, Huijuan Bi, Wei Yan, Ning Yang, Lujiang Qu
Software Mentions: 4
Published: about 9 years ago

10.1186/s12864-015-2318-2

Transcriptome profiling of soybean (Glycine max) roots challenged with pathogenic and non-pathogenic isolates of Fusarium oxysporum
Cited by: 56
Author(s): Alessandra Lanubile, Usha Muppirala, Andrew J. Severin, Adriano Marocco, Gary P. Munkvold
Software Mentions: 3
Published: almost 9 years ago

10.3389/fpls.2015.00536

TAL effectors and activation of predicted host targets distinguish Asian from African strains of the rice pathogen Xanthomonas oryzae pv. oryzicola while strict conservation suggests universal importance of five TAL effectors
Cited by: 79
Author(s): Katherine Wilkins, Nicholas J. Booher, Li Wang, Adam J. Bogdanove
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2164-15-1084

RNA-seq analysis of broiler liver transcriptome reveals novel responses to high ambient temperature
Cited by: 72
Author(s): Derrick Coble, Damarius S. Fleming, Michael E. Persia, C. M. Ashwell, Max F. Rothschild, Carl J. Schmidt, Susan J. Lamont
Software Mentions: 2
Published: almost 11 years ago

10.1128/mBio.00709-17

The In-Feed Antibiotic Carbadox Induces Phage Gene Transcription in the Swine Gut Microbiome
Cited by: 35
Author(s): Timothy A. Johnson, Torey Looft, Andrew J. Severin, Darrell O. Bayles, Daniel J. Nasko, K. Eric Wommack, Adina Howe, Heather K. Allen
Software Mentions: 2
Published: about 7 years ago

10.1186/s12864-016-2395-x

Post-weaning blood transcriptomic differences between Yorkshire pigs divergently selected for residual feed intake
Cited by: 20
Author(s): Haibo Li, Yet Nguyen, Dan Nettleton, Jack C. M. Dekkers, Christopher K. Tuggle
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12864-015-1844-2

Transcriptional analysis of phloem-associated cells of potato
Cited by: 12
Author(s): Tong Lin, Coralie C. Lashbrook, Sung-Ki Cho, Nathaniel M. Butler, Pooja Sharma, Usha Muppirala, Andrew J. Severin, David J. Hannapel
Software Mentions: 2
Published: about 9 years ago

10.1007/s13253-015-0226-1

Detecting Differentially Expressed Genes with RNA-seq Data Using Backward Selection to Account for the Effects of Relevant Covariates
Cited by: 6
Author(s): Yet Nguyen, Dan Nettleton, Haibo Li, Christopher K. Tuggle
Software Mentions: 2
Published: about 9 years ago

10.1186/s12867-018-0118-3

MiRNAs differentially expressed in skeletal muscle of animals with divergent estimated breeding values for beef tenderness
Cited by: 19
Author(s): Berna Inés Giménez Kappeler, Luciana Correia de Almeida Regitano, Mirele Daiana Poleti, Aline Silva Mello Cesar, Gabriel Costa Monteiro Moreira, G. Gasparin
Software Mentions: 1
Published: almost 6 years ago

10.1093/jxb/eru249

The Aux/IAA gene rum1 involved in seminal and lateral root formation controls vascular patterning in maize (Zea mays L.) primary roots
Cited by: 62
Author(s): Yanxiang Zhang, Anja Paschold, Caroline Marcon, Sanzhen Liu, Huanhuan Tai, Josefine Nestler, Cheng‐Ting Yeh, Nina Opitz, Christa Lanz, Patrick S. Schnable, Frank Hochholdinger
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0082333

The Maize glossy13 Gene, Cloned via BSR-Seq and Seq-Walking Encodes a Putative ABC Transporter Required for the Normal Accumulation of Epicuticular Waxes
Cited by: 70
Author(s): Li Li, Delin Li, Sanzhen Liu, Xiaoli Ma, Charles R. Dietrich, Heng-Cheng Hu, Gaisheng Zhang, Zhiyong Liu, Jun Zheng, Guoying Wang, Patrick S. Schnable
Software Mentions: 1
Published: almost 11 years ago