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: pypi: NucleoATAC

https://packages.ecosyste.ms/registries/pypi.org/packages/NucleoATAC

python package for calling nucleosomes with ATAC-Seq
1 version
Latest release: over 7 years ago
11 downloads last month

Papers Mentioning NucleoATAC 17

10.1186/s13059-020-1929-3

From reads to insight: a hitchhiker’s guide to ATAC-seq data analysis
Cited by: 231
Author(s): Feng Yan, David Powell, David Curtis, Nicholas C. Wong
Software Mentions: 21
Published: over 4 years ago

ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data
Cited by: 133
Author(s): Jianhong Ou, Haibo Li, Jun Yu, Michelle A. Kelliher, Lucio H. Castilla, Nathan D. Lawson, Lihua Julie Zhu
Software Mentions: 14
Published: over 6 years ago

10.1038/s41598-020-80165-9

Multi-level remodelling of chromatin underlying activation of human T cells
Cited by: 23
Author(s): Naiara G. Bediaga, Hannah D. Coughlan, Timothy M. Johanson, Alexandra L. Garnham, Gaetano Naselli, Jan Schröder, Liam G. Fearnley, Esther Bandala‐Sanchez, Rhys S. Allan, Gordon K. Smyth, Leonard C. Harrison
Software Mentions: 14
Published: over 3 years ago

10.1016/j.devcel.2018.11.009

From Pioneer to Repressor: Bimodal foxd3 Activity Dynamically Remodels Neural Crest Regulatory Landscape In Vivo
Cited by: 90
Author(s): Martyna Lukoseviciute, Daria Gavriouchkina, Ruth M. Williams, Tatiana Hochgreb-Hägele, Upeka Senanayake, Vanessa Chong, Supat Thongjuea, Emmanouela Repapi, Adam J. Mead, Tatjana Sauka‐Spengler
Software Mentions: 11
Published: almost 6 years ago

10.3390/jof6030182

ATAC-Seq Identifies Chromatin Landscapes Linked to the Regulation of Oxidative Stress in the Human Fungal Pathogen Candida albicans
Cited by: 14
Author(s): Sabrina Jenull, Michael Tscherner, Theresia Mair, Karl Kuchler
Software Mentions: 9
Published: almost 4 years ago

10.7554/eLife.22631

The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cells
Cited by: 184
Author(s): Hamish W King, Robert J. Klose
Software Mentions: 7
Published: over 7 years ago

10.3389/fgene.2018.00250

GUAVA: A Graphical User Interface for the Analysis and Visualization of ATAC-seq Data
Cited by: 15
Author(s): Mayur Divate, Edwin Cheung
Software Mentions: 7
Published: about 6 years ago

10.1186/s13059-020-02156-3

STARR-seq identifies active, chromatin-masked, and dormant enhancers in pluripotent mouse embryonic stem cells
Cited by: 42
Author(s): Tianran Peng, Yanan Zhai, Yaser Atlasi, Menno ter Huurne, Hendrik Marks, Hendrik G. Stunnenberg, Wout Megchelenbrink
Software Mentions: 7
Published: about 4 years ago

10.7554/eLife.59610

Odd-paired is a pioneer-like factor that coordinates with Zelda to control gene expression in embryos
Cited by: 29
Author(s): Theodora Koromila, Fan Gao, Yohei Iwasaki, Peng He, Lior Pachter, J. Peter Gergen, Angelike Stathopoulos
Software Mentions: 7
Published: about 4 years ago

10.7554/eLife.28275

Concentration dependent chromatin states induced by the bicoid morphogen gradient
Cited by: 76
Author(s): Colleen E Hannon, Shelby A. Blythe, Eric Wieschaus
Software Mentions: 7
Published: about 7 years ago

10.3389/fcell.2020.00553

ADNP Controls Gene Expression Through Local Chromatin Architecture by Association With BRG1 and CHD4
Cited by: 22
Author(s): Xiaoyun Sun, Wenjun Yu, Li Li, Yuhua Sun
Software Mentions: 6
Published: about 4 years ago

10.3389/fgene.2020.618478

ATACgraph: Profiling Genome-Wide Chromatin Accessibility From ATAC-seq
Cited by: 7
Author(s): Rita Jui-Hsien Lu, Yen-Ting Liu, Chih-Wei Huang, Ming‐Ren Yen, Chung‐Yen Lin, Pao‐Yang Chen
Software Mentions: 4
Published: over 3 years ago

10.7554/eLife.39911

A new experimental platform facilitates assessment of the transcriptional and chromatin landscapes of aging yeast
Cited by: 55
Author(s): David G. Hendrickson, Ilya Soifer, Bernd J. Wranik, Griffin Kim, Michael Robles, Patrick A. Gibney, R. Scott McIsaac
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-018-33779-z

Chromatin accessibility landscape of articular knee cartilage reveals aberrant enhancer regulation in osteoarthritis
Cited by: 34
Author(s): Ye Liu, Jen-Chien Chang, Chung-Chau Hon, Naoshi Fukui, Nobuhiro Tanaka, Zhen Ya Zhang, Ming Ta Michael Lee, Aki Minoda
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-019-41639-7

Hox gene expression determines cell fate of adult periosteal stem/progenitor cells
Cited by: 22
Author(s): Vivian Bradaschia-Corrêa, Kevin Leclerc, Anne Marie Josephson, Sooyeon Lee, Laura Palma, Hannah P. Litwa, Shane S. Neibart, Jason C. Huo, Philipp Leucht
Software Mentions: 3
Published: over 5 years ago

10.7554/eLife.20148

Establishment and maintenance of heritable chromatin structure during early Drosophila embryogenesis
Cited by: 135
Author(s): Shelby A. Blythe, Eric Wieschaus
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41598-018-29775-y

Age Alters Chromatin Structure and Expression of SUMO Proteins under Stress Conditions in Human Adipose-Derived Stem Cells
Cited by: 16
Author(s): Xiaoyin Shan, Cleresa Roberts, Yemin Lan, Ivona Percec
Software Mentions: 1
Published: about 6 years ago