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: cqn

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

Conditional quantile normalization
1 version
Latest release: about 1 year ago
4 dependent packages
46,957 downloads total

Papers Mentioning cqn 14

KRAS mutant rectal cancer cells interact with surrounding fibroblasts to deplete the extracellular matrix
Cited by: 6
Author(s): Jin K. Kim, Michael R. Marco, Seo‐Hyun Choi, Xuan Qu, Chin-Tung Chen, Moshe Elkabets, Lauren Fairchild, Oliver Chow, Francisco M. Barriga, Lukas E. Dow, Kevin P. O’Rourke, Bryan Szeglin, Dmitry Yarilin, Sho Fujisawa, Katia Manova‐Todorova, Philip B. Paty, Jinru Shia, Christina Leslie, J. Joshua Smith, Scott W. Lowe, Raphael Pelossof, Francisco Sánchez-Vega, Julio García-Aguilar
Software Mentions: 18
Published: over 3 years ago

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: almost 10 years ago

10.12688/wellcomeopenres.16430.2

Polysomal mRNA Association and Gene Expression in Trypanosoma brucei
Cited by: 0
Author(s): Michele Tinti, Anna Kelner-Mirôn, Lizzie J. Marriott, Michael A. J. Ferguson
Software Mentions: 11
Published: about 3 years ago

10.1186/s13059-016-1000-6

Blood lipids influence DNA methylation in circulating cells
Cited by: 149
Author(s): Koen F. Dekkers, Maarten van Iterson, Roderick C. Slieker, Matthijs Moed, Marc Jan Bonder, M.A. van Galen, Hailiang Mei, Daria V. Zhernakova, Leonard H van den Berg, Joris Deelen, Jenny van Dongen, Diana van Heemst, Albert Hofman, Jouke Jan Hottenga, Carla Kallen, Casper G. Schalkwijk, Coen D. A. Stehouwer, Ettje F. Tigchelaar, André G. Uitterlinden, Gonneke Willemsen, Alexandra Zhernakova, Lude Franke, Peter A.C. ’t Hoen, Ritsert C. Jansen, Joyce B. J. van Meurs, Dorret I. Boomsma, Cornelia M. van Duijn, Marleen M.J. van Greevenbroek, Jan H. Veldink, Cisca Wijmenga, Erik W. van Zwet, P. Eline Slagboom, J. Wouter Jukema, Bastiaan T. Heijmans
Software Mentions: 9
Published: over 8 years ago

10.1186/1471-2105-14-254

A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments
Cited by: 49
Author(s): Mikel Esnaola, Pedro Puig, David Herrera González, Robert Castelo, Juan R. González
Software Mentions: 9
Published: over 11 years ago

10.1038/s41597-019-0183-6

CommonMind Consortium provides transcriptomic and epigenomic data for Schizophrenia and Bipolar Disorder
Cited by: 127
Author(s): Gabriel E. Hoffman, Jaroslav Bendl, Georgios Voloudakis, Kelsey S. Montgomery, Laura Sloofman, Ying-Chih Wang, Hardik Shah, Mads E. Hauberg, Jessica Johnson, Kiran Girdhar, Lingyun Song, John F. Fullard, Robin Kramer, Chang-Gyu Hahn, Raquel E. Gur, Stefano Marenco, Barbara K. Lipska, David A. Lewis, Vahram Haroutunian, Scott E. Hemby, Patrick F. Sullivan, Schahram Akbarian, Andrew Chess, Joseph D. Buxbaum, Greg Crawford, Enrico Domenici, Bernie Devlin, Solveig K. Sieberts, Mette A. Peters, Panos Roussos
Software Mentions: 8
Published: about 5 years ago

10.1371/journal.pbio.3000481

Recurrent functional misinterpretation of RNA-seq data caused by sample-specific gene length bias
Cited by: 45
Author(s): Shir Mandelboum, Zohar Manber, Orna Elroy‐Stein, Ran Elkon
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-017-16747-x

CMScaller: an R package for consensus molecular subtyping of colorectal cancer pre-clinical models
Cited by: 193
Author(s): Peter W. Eide, Jarle Bruun, Ragnhild Lothe, Anita Sveen
Software Mentions: 4
Published: almost 7 years ago

10.1186/s13059-019-1866-1

547 transcriptomes from 44 brain areas reveal features of the aging brain in non-human primates
Cited by: 25
Author(s): Mingli Li, Shihao Wu, Jinjin Zhang, Hang-Yu Tian, Yong Shao, Zhengbo Wang, David M. Irwin, Jiali Li, Xintian Hu, Dongdong Wu
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0212127

Leukemia multiclass assessment and classification from Microarray and RNA-seq technologies integration at gene expression level
Cited by: 29
Author(s): Daniel Castillo, Juan Manuel Gálvez, José Benavente Herrera, Fernando Rojas, Olga Valenzuela, Octavio Caba, José Luis Paniza Prados, Ignacio Rojas
Software Mentions: 2
Published: almost 6 years ago

10.1093/molbev/msu226

Transcript Length Mediates Developmental Timing of Gene Expression Across Drosophila
Cited by: 51
Author(s): Carlo G. Artieri, Hunter B. Fraser
Software Mentions: 2
Published: over 10 years ago

10.1186/s12859-017-1925-0

Integration of RNA-Seq data with heterogeneous microarray data for breast cancer profiling
Cited by: 38
Author(s): Daniel Castillo, Juan Manuel Gálvez, José Benavente Herrera, Belén San Román, Fernando Rojas, Ignacio Rojas
Software Mentions: 2
Published: about 7 years ago

10.1186/s12881-015-0254-2

Expression analysis of the osteoarthritis genetic susceptibility locus mapping to an intron of the MCF2L gene and marked by the polymorphism rs11842874
Cited by: 18
Author(s): Colin Shepherd, Andrew Skelton, Michael D. Rushton, Louise N. Reynard, John Loughlin
Software Mentions: 2
Published: about 9 years ago

10.1186/s13072-018-0191-3

Age-related DNA methylation changes are tissue-specific with ELOVL2 promoter methylation as exception
Cited by: 121
Author(s): Roderick C. Slieker, Caroline L Relton, Tom R. Gaunt, P. Eline Slagboom, Bastiaan T. Heijmans
Software Mentions: 1
Published: over 6 years ago