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: easyRNASeq

https://packages.ecosyste.ms/registries/bioconductor.org/packages/easyRNASeq

Count summarization and normalization for RNA-Seq data
1 version
Latest release: about 1 year ago
1 dependent package
50,084 downloads total

Papers Mentioning easyRNASeq 17

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: about 10 years ago

10.1186/s12859-021-04211-7

RNAdetector: a free user-friendly stand-alone and cloud-based system for RNA-Seq data analysis
Cited by: 6
Author(s): Alessandro La Ferlita, Salvatore Alaimo, Sebastiano Di Bella, Emanuele Martorana, Georgios I. Laliotis, Francesco Bertoni, Luciano Cascione, Philip N. Tsichlis, Alfredo Ferro, Roberta Bosotti, Alfredo Pulvirenti
Software Mentions: 10
Published: over 3 years ago

10.1093/bioinformatics/bts477

easyRNASeq: a bioconductor package for processing RNA-Seq data
Cited by: 96
Author(s): Nicolas Delhomme, Ismaël Padioleau, Eileen E. M. Furlong, Lars M. Steinmetz
Software Mentions: 9
Published: over 12 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: almost 13 years ago

10.1186/1471-2229-13-213

Ups and downs of a transcriptional landscape shape iron deficiency associated chlorosis of the maize inbreds B73 and Mo17
Cited by: 12
Author(s): Claude Urbany, Andreas Benke, Johanna Marsian, Bruno Huettel, Richard Reinhardt, Benjamin Stich
Software Mentions: 7
Published: about 11 years ago

10.1038/s41598-019-44266-4

Transcriptomics Analysis Reveals New Insights into the Roles of Notch1 Signaling on Macrophage Polarization
Cited by: 21
Author(s): Chetan P. Hans, Neekun Sharma, Sidharth Sen, Shuai Zeng, Rishabh Dev, Yuyong Jiang, Advitiya Mahajan, Trupti Joshi
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0233543

A transcriptome-based approach to identify functional modules within and across primary human immune cells
Cited by: 10
Author(s): Saraï Mola, Sylvain Foisy, Gabrielle Boucher, François Major, Claudine Beauchamp, Mohamad Karaky, Philippe Goyette, Sylvie Lesage, John D. Rioux
Software Mentions: 4
Published: over 4 years ago

10.1186/s12864-017-3608-7

Sex differences in the molecular signature of the developing mouse hippocampus
Cited by: 40
Author(s): Joseph L. Bundy, Cynthia Vied, Richard S. Nowakowski
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pone.0122396

Integration of Transcriptome and Whole Genomic Resequencing Data to Identify Key Genes Affecting Swine Fat Deposition
Cited by: 19
Author(s): Kai Xing, Feng Zhu, Lichao Zhai, Huijie Liu, Yuan Wang, Zhijun Wang, Shaokang Chen, Zhuocheng Hou, Chuduan Wang
Software Mentions: 3
Published: over 9 years ago

10.3389/fcvm.2018.00030

Postnatal and Adult Aortic Heart Valves Have Distinctive Transcriptional Profiles Associated With Valve Tissue Growth and Maintenance Respectively
Cited by: 10
Author(s): Emily Nordquist, Stephanie LaHaye, Casey Nagel, Joy Lincoln
Software Mentions: 3
Published: over 6 years ago

10.3389/fendo.2018.00245

Drosophila Insulin-Like Peptides DILP2 and DILP5 Differentially Stimulate Cell Signaling and Glycogen Phosphorylase to Regulate Longevity
Cited by: 65
Author(s): Stephanie Post, Galina Karashchuk, John D. Wade, Waseem Sajid, Pierre De Meyts, Marc Tatar
Software Mentions: 3
Published: over 6 years ago

10.1534/g3.115.020982

An Examination of Dynamic Gene Expression Changes in the Mouse Brain During Pregnancy and the Postpartum Period
Cited by: 42
Author(s): Surjyendu Ray, Ruei-Ying Tzeng, Lisa M. DiCarlo, Joseph L. Bundy, Cynthia Vied, Gary Tyson, Richard S. Nowakowski, Michelle N. Arbeitman
Software Mentions: 3
Published: almost 9 years ago

10.1038/srep23219

Identification of genes for controlling swine adipose deposition by integrating transcriptome, whole-genome resequencing, and quantitative trait loci data
Cited by: 42
Author(s): Kai Xing, Feng Zhu, Lichao Zhai, ShaoKang Chen, Zhen Tan, Yangyang Sun, Zhuocheng Hou, ChuDuan Wang
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12864-015-1282-1

Genome-wide expression profiling and phenotypic evaluation of European maize inbreds at seedling stage in response to heat stress
Cited by: 79
Author(s): Felix P. Frey, Claude Urbany, Bruno Hüttel, Richard Reinhardt, Benjamin Stich
Software Mentions: 2
Published: almost 10 years ago

10.1002/1878-0261.12973

Systematic analysis of migration factors by MigExpress identifies essential cell migration control genes in non‐small cell lung cancer
Cited by: 5
Author(s): Jagriti Pal, Andrea C. Becker, Sonam Dhamija, Jeanette Seiler, Mahmoud Abdelkarim, Yogita Sharma, Jürgen Behr, Chen Meng, Christina Ludwig, Bernhard Küster, Sven Diederichs
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-016-0025-0

The complete 12 Mb genome and transcriptome of Nonomuraea gerenzanensis with new insights into its duplicated “magic” RNA polymerase
Cited by: 35
Author(s): Valeria D’Argenio, Mauro Petrillo, Daniela Pasanisi, Caterina Pagliarulo, Roberta Colicchio, Adelfia Talà, Maria Stella de Biase, Mario Zanfardino, Emanuela Scolamiero, Chiara Pagliuca, Antonio Gaballo, Annunziata Gaetana Cicatiello, Piergiuseppe Cantiello, Irene Postiglione, Barbara Naso, Angelo Boccia, Miriana Durante, Luca Cozzuto, Paola Salvatore, Giovanni Paolella, Francesco Salvatore, Pietro Alifano
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0101425

RNA-Seq Analysis to Identify Novel Roles of Scleraxis during Embryonic Mouse Heart Valve Remodeling
Cited by: 11
Author(s): Damien N. Barnette, Matthew VandeKopple, Yonggan Wu, David A. Willoughby, Joy Lincoln
Software Mentions: 1
Published: over 10 years ago