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: GOTHiC

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

Binomial test for Hi-C data analysis
1 version
Latest release: about 1 year ago
20,576 downloads total

Papers Mentioning GOTHiC 17

10.1186/s13072-021-00390-y

Molecular and computational approaches to map regulatory elements in 3D chromatin structure
Cited by: 7
Author(s): Beoung Hun Lee, Suhn Kyong Rhie
Software Mentions: 21
Published: over 3 years ago

GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data
Cited by: 54
Author(s): Nathan Harmston, Elizabeth Ing-Simmons, Malcolm Perry, Anja Barešić, Boris Lenhard
Software Mentions: 15
Published: about 9 years ago

10.1007/s12551-018-0489-1

Hi-C analysis: from data generation to integration
Cited by: 62
Author(s): Koustav Pal, Mattia Forcato, Francesco Ferrari
Software Mentions: 8
Published: almost 6 years ago

10.1186/s13059-019-1868-z

MIA-Sig: multiplex chromatin interaction analysis by signal processing and statistical algorithms
Cited by: 9
Author(s): Minji Kim, Meizhen Zheng, Simon Zhongyuan Tian, Byoungkoo Lee, Jeffrey H. Chuang, Yijun Ruan
Software Mentions: 7
Published: almost 5 years ago

10.1371/journal.ppat.1009875

Short- and long-range cis interactions between integrated HPV genomes and cellular chromatin dysregulate host gene expression in early cervical carcinogenesis
Cited by: 14
Author(s): Ian J. Groves, Emma L A Drane, Marco Michalski, Jack Monahan, Cinzia G. Scarpini, Stephen Smith, Giovanni Bussotti, Csilla Várnai, Stefan Schoenfelder, Peter Fraser, Anton J. Enright, Nicholas Coleman
Software Mentions: 6
Published: about 3 years ago

10.1186/s13072-021-00417-4

Seeing the forest through the trees: prioritising potentially functional interactions from Hi-C
Cited by: 2
Author(s): Ning Liu, Wai Yee Low, Hamid Alinejad‐Rokny, Stephen Pederson, Timothy Sadlon, Simon C. Barry, James Breen
Software Mentions: 5
Published: about 3 years ago

10.1186/s13059-019-1706-3

ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C
Cited by: 25
Author(s): Yousra Ben Zouari, Anne Molitor, Natalia Sikorska, Véra Pancaldi, Tom Sexton
Software Mentions: 4
Published: over 5 years ago

10.1128/JVI.01413-17

The Epstein-Barr Virus Episome Maneuvers between Nuclear Chromatin Compartments during Reactivation
Cited by: 41
Author(s): S. Moquin, Sean Thomas, Sean Whalen, Alix Warburton, Samantha G. Fernandez, Alison A. McBride, Katherine S. Pollard, JJ L. Miranda
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-021-07373-z

Inferring time series chromatin states for promoter-enhancer pairs based on Hi-C data
Cited by: 2
Author(s): Henriette Miko, Yunjiang Qiu, Bjoern Gaertner, Maike Sander, Uwe Ohler
Software Mentions: 3
Published: almost 4 years ago

10.1016/j.celrep.2019.08.040

RUNX1-ETO Depletion in t(8;21) AML Leads to C/EBPα- and AP-1-Mediated Alterations in Enhancer-Promoter Interaction
Cited by: 23
Author(s): Anetta Ptasińska, Anna Pickin, Salam A. Assi, Paulynn Suyin Chin, Luke Ames, Roberto Avellino, Stephan Gröschel, Ruud Delwel, Peter N. Cockerill, Cameron S. Osborne, Constanze Bonifer
Software Mentions: 3
Published: about 5 years ago

10.1186/s13059-019-1904-z

CHROMATIX: computing the functional landscape of many-body chromatin interactions in transcriptionally active loci from deconvolved single cells
Cited by: 21
Author(s): Alan Perez-Rathke, Qiu Sun, Boshen Wang, Valentina Boeva, Zongshu Shao, Jie Liang
Software Mentions: 3
Published: almost 5 years ago

10.1007/s10577-016-9546-4

Capturing genomic relationships that matter
Cited by: 3
Author(s): Cameron S. Osborne, Borbála Mifsud
Software Mentions: 2
Published: almost 8 years ago

10.1186/s13059-020-02061-9

3DeFDR: statistical methods for identifying cell type-specific looping interactions in 5C and Hi-C data
Cited by: 11
Author(s): Lindsey R. Fernandez, Thomas G. Gilgenast, Jennifer E. Phillips-Cremins
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0177280

Correction: GOTHiC, a probabilistic model to resolve complex biases and to identify real interactions in Hi-C data
Cited by: 0
Author(s):
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-020-6636-7

MHiC, an integrated user-friendly tool for the identification and visualization of significant interactions in Hi-C data
Cited by: 10
Author(s): Saman Khakmardan, Mohsen Rezvani, Ali A. Pouyan, Mansoor Fateh, Hamid Alinejad‐Rokny
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0174744

GOTHiC, a probabilistic model to resolve complex biases and to identify real interactions in Hi-C data
Cited by: 53
Author(s): Borbála Mifsud, Iñigo Martincorena, Élodie Darbo, R. Sugar, Stefan Schoenfelder, Peter Fraser, Nicholas M. Luscombe
Software Mentions: 1
Published: over 7 years ago

10.12688/f1000research.7334.1

HiCUP: pipeline for mapping and processing Hi-C data
Cited by: 451
Author(s): Steven W. Wingett, Philip Ewels, Mayra Furlan-Magaril, Takashi Nagano, Stefan Schoenfelder, Peter Fraser, Simon Andrews
Software Mentions: 1
Published: about 9 years ago