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: HiCseg

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

Detection of domains in HiC data
2 versions
Latest release: over 10 years ago
1 dependent package
201 downloads last month

Papers Mentioning HiCseg 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: almost 4 years ago

HiCeekR: A Novel Shiny App for Hi-C Data Analysis
Cited by: 13
Author(s): Lucio Di Filippo, Dario Righelli, Miriam Gagliardi, Maria R. Matarazzo, Claudia Angelini
Software Mentions: 12
Published: about 5 years ago

10.1186/s13059-018-1596-9

Comparison of computational methods for the identification of topologically associating domains
Cited by: 155
Author(s): Marie Zufferey, Daniele Tavernari, Elisa Oricchio, Giovanni Ciriello
Software Mentions: 9
Published: about 6 years ago

10.1016/j.cell.2017.04.013

The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension
Cited by: 607
Author(s): Judith H.I. Haarhuis, Robin H. van der Weide, Vincent A. Blomen, J. Omar Yáñez-Cuna, Mario Amendola, Marjon S. van Ruiten, Peter H.L. Krijger, Hans Teunissen, René H. Medema, Bas van Steensel, Thijn R. Brummelkamp, Elzo de Wit, Benjamin D. Rowland
Software Mentions: 8
Published: over 7 years ago

10.1093/bioinformatics/btaa555

Benchmark of software tools for prokaryotic chromosomal interaction domain identification
Cited by: 3
Author(s): Mikhail D. Magnitov, Veronika S Kuznetsova, Sergey V. Ulianov, Sergey V. Razin, Alexander Tyakht
Software Mentions: 8
Published: over 4 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: about 6 years ago

10.1186/s12859-020-03652-w

SpectralTAD: an R package for defining a hierarchy of topologically associated domains using spectral clustering
Cited by: 22
Author(s): Kellen Garrison Cresswell, John C. Stansfield, Mikhail G. Dozmorov
Software Mentions: 7
Published: over 4 years ago

10.1186/s13059-021-02435-7

DeTOKI identifies and characterizes the dynamics of chromatin TAD-like domains in a single cell
Cited by: 15
Author(s): Xiao Li, Guangjie Zeng, Angsheng Li, Zhihua Zhang
Software Mentions: 6
Published: over 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: over 3 years ago

10.1186/s12859-015-0678-x

HiCdat: a fast and easy-to-use Hi-C data analysis tool
Cited by: 45
Author(s): Marc W. Schmid, Stefan Grob, Ueli Grossniklaus
Software Mentions: 5
Published: over 9 years ago

10.1186/s13059-021-02378-z

GRiNCH: simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization
Cited by: 14
Author(s): Da-Inn Lee, Sushmita Roy
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0191899

Sequence-based multiscale modeling for high-throughput chromosome conformation capture (Hi-C) data analysis
Cited by: 3
Author(s): Kelin Xia
Software Mentions: 1
Published: almost 7 years ago

10.1186/s13059-018-1486-1

HiGlass: web-based visual exploration and analysis of genome interaction maps
Cited by: 702
Author(s): Peter Kerpedjiev, Nezar Abdennur, Fritz Lekschas, Chuck McCallum, Kasper Dinkla, Hendrik Strobelt, Jacob M. Luber, Scott Ouellette, Alaleh Azhir, Nikhil Kumar, Jeewon Hwang, Soohyun Lee, B. Alver, Hanspeter Pfister, Leonid A. Mirny, Peter J. Park, Nils Gehlenborg
Software Mentions: 1
Published: over 6 years ago

10.1186/s13059-015-0745-7

Analysis methods for studying the 3D architecture of the genome
Cited by: 146
Author(s): Ferhat Ay, William Stafford Noble
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pcbi.1004908

Computational Identification of Genomic Features That Influence 3D Chromatin Domain Formation
Cited by: 27
Author(s): Raphaël Mourad, Olivier Cuvier
Software Mentions: 1
Published: over 8 years ago

10.1186/s12920-019-0574-8

Enhancer variants associated with Alzheimer’s disease affect gene expression via chromatin looping
Cited by: 50
Author(s): Masataka Kikuchi, Norikazu Hara, M. Hasegawa, Akinori Miyashita, Ryozo Kuwano, Takeshi Ikeuchi, Akihiro Nakaya
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-019-6303-z

A computational method to predict topologically associating domain boundaries combining histone Marks and sequence information
Cited by: 10
Author(s): Wei Gan, Juan Luo, Yi Zhou Li, Xiaoyu Gu, Min Zhu, Meng Long Li
Software Mentions: 1
Published: about 5 years ago