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: shinyMethyl

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

Interactive visualization for Illumina methylation arrays
1 version
Latest release: about 1 year ago
21,607 downloads total

Papers Mentioning shinyMethyl 18

10.3390/jcm9041055

Whole-Genome DNA Methylation Profiling of CD14+ Monocytes Reveals Disease Status and Activity Differences in Crohn’s Disease Patients
Cited by: 12
Author(s): Andrew Y. Li Yim, Nicolette W. Duijvis, Mohammed Ghiboub, Catriona Sharp, Enrico Ferrero, Marcel M.A.M. Mannens, Geert D’Haens, Wouter J. de Jonge, Anje A. te Velde, Peter Henneman
Software Mentions: 11
Published: over 4 years ago

10.1038/s41598-019-44765-4

Monozygotic twins and triplets discordant for amyotrophic lateral sclerosis display differential methylation and gene expression
Cited by: 35
Author(s): Ingrid Tarr, Emma McCann, Beben Benyamin, Timothy J. Peters, Natalie A. Twine, Katharine Y. Zhang, Qiongyi Zhao, Zong Hong Zhang, Dominic B. Rowe, Garth A. Nicholson, Denis C. Bauer, Susan J. Clark, Ian P. Blair, Kelly L. Williams
Software Mentions: 11
Published: over 5 years ago

10.12688/f1000research.14966.1

iSEE: Interactive SummarizedExperiment Explorer
Cited by: 68
Author(s): Kévin Rue-Albrecht, Fédérico Marini, Charlotte Soneson, Aaron T. L. Lun
Software Mentions: 9
Published: over 6 years ago

10.1186/s12864-018-4766-y

BoostMe accurately predicts DNA methylation values in whole-genome bisulfite sequencing of multiple human tissues
Cited by: 32
Author(s): Luli S. Zou, Michael R. Erdos, D. Leland Taylor, Peter S. Chines, Arushi Varshney, Stephen C. J. Parker, Francis S. Collins, John P. Didion
Software Mentions: 8
Published: over 6 years ago

10.12688/f1000research.4680.2

shinyMethyl: interactive quality control of Illumina 450k DNA methylation arrays in R
Cited by: 96
Author(s): Jean Philippe Fortin, Elana J. Fertig, Kasper D. Hansen
Software Mentions: 6
Published: over 10 years ago

10.1186/s13059-015-0741-y

Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data
Cited by: 222
Author(s): Jean Philippe Fortin, Kasper D. Hansen
Software Mentions: 6
Published: over 9 years ago

10.1186/s13059-014-0503-2

Functional normalization of 450k methylation array data improves replication in large cancer studies
Cited by: 640
Author(s): Jean Philippe Fortin, Aurélie Labbe, Mathieu Lemire, Brent W. Zanke, Thomas J. Hudson, Elana J. Fertig, Celia M.T. Greenwood, Kasper D. Hansen
Software Mentions: 6
Published: about 10 years ago

10.1038/s41598-017-14788-w

Smoking induces DNA methylation changes in Multiple Sclerosis patients with exposure-response relationship
Cited by: 50
Author(s): Francesco Marabita, Malin Almgren, Louise K. Sjöholm, Lara Kular, Yun Liu, Tojo James, Nimrod Kiss, Andrew P. Feinberg, Tomas Olsson, Ingrid Kockum, Lars Alfredsson, Tomas J. Ekström, Maja Jagodic
Software Mentions: 6
Published: about 7 years ago

10.1186/s13029-019-0071-7

eUTOPIA: solUTion for Omics data PreprocessIng and Analysis
Cited by: 34
Author(s): Veer Singh Marwah, Giovanni Scala, Pia Anneli Sofia Kinaret, Angela Serra, Harri Alenius, Vittorio Fortino, Dario Greco
Software Mentions: 5
Published: almost 6 years ago

10.3389/fgene.2019.00770

Maternal Smoking During Pregnancy Induces Persistent Epigenetic Changes Into Adolescence, Independent of Postnatal Smoke Exposure and Is Associated With Cardiometabolic Risk
Cited by: 65
Author(s): Sebastian Rauschert, Phillip E. Melton, Graham C. Burdge, Jeffrey M. Craig, Keith M. Godfrey, Joanna D. Holbrook, Karen A. Lillycrop, Trevor A. Mori, Lawrence J. Beilin, Wendy H. Oddy, Craig E. Pennell, Rae‐Chi Huang
Software Mentions: 5
Published: over 5 years ago

10.7554/eLife.29156

Major transcriptional changes observed in the Fulani, an ethnic group less susceptible to malaria
Cited by: 33
Author(s): Jaclyn Quin, Ioana Bujila, Mariama Chérif, Guillaume S. Sanou, Ying Qu, Manijeh Vafa Homann, Anna Rolicka, Sodiomon B. Sirima, Mary A. O’Connell, Andreas Lennartsson, Marita Troye‐Blomberg, Issa Nébié, Ann‐Kristin Östlund Farrants
Software Mentions: 4
Published: over 7 years ago

10.1186/s13148-018-0504-1

Identifying mislabeled and contaminated DNA methylation microarray data: an extended quality control toolset with examples from GEO
Cited by: 82
Author(s): Jonathan Heiss, Allan C. Just
Software Mentions: 4
Published: over 6 years ago

10.1093/bioinformatics/bty476

Meffil: efficient normalization and analysis of very large DNA methylation datasets
Cited by: 173
Author(s): Josine L. Min, Gibran Hemani, George Davey Smith, Caroline L Relton, Matthew Suderman
Software Mentions: 4
Published: over 6 years ago

10.1093/bioinformatics/btw691

Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi
Cited by: 470
Author(s): Jean Philippe Fortin, Timothy J. Triche, Kasper D. Hansen
Software Mentions: 3
Published: about 8 years ago

10.3389/fnbeh.2018.00125

Prenatal Alcohol Exposure Is Associated With Adverse Cognitive Effects and Distinct Whole-Genome DNA Methylation Patterns in Primary School Children
Cited by: 18
Author(s): Stefan Frey, Anna Eichler, Valeska Stonawski, Jennifer Kriebel, Simone Wahl, Sabina Gallati, Tamme W. Goecke, Peter A. Fasching, Matthias W. Beckmann, Oliver Kratz, Gunther H. Moll, Hartmut Heinrich, Johannes Kornhuber, Yulia Golub
Software Mentions: 2
Published: over 6 years ago

10.12688/wellcomeopenres.15136.1

Assessment of dried blood spots for DNA methylation profiling
Cited by: 18
Author(s): Richard M Martin, Louise MacGillivray, Sarah McCafferty, Nicola Wrobel, Lee Murphy, Shona M. Kerr, Stewart W. Morris, Archie Campbell, Andrew M. McIntosh, David J. Porteous, Kathryn Evans
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pgen.1009750

Genome-wide methylation data improves dissection of the effect of smoking on body mass index
Cited by: 5
Author(s): Carmen Amador, Yanni Zeng, M. Barber, Richard M Martin, Archie Campbell, Andrew M. McIntosh, Kathryn Evans, David J. Porteous, Caroline Hayward, James F. Wilson, Pau Navarro, Chris Haley
Software Mentions: 2
Published: over 3 years ago

10.18632/aging.203117

Different epigenetic signatures of newborn telomere length and telomere attrition rate in early life
Cited by: 11
Author(s): Congrong Wang, Tim S. Nawrot, Charlotte Van Der Stukken, Dominika Tylus, Hanne Sleurs, Martien Peusens, Rossella Alfano, Sabine A. S. Langie, Michelle Plusquin, Dries S. Martens
Software Mentions: 2
Published: over 3 years ago