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: almost 8 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 analysisCited by: 231
Author(s): Feng Yan, David Powell, David Curtis, Nicholas C. Wong
Software Mentions: 21
Published: almost 5 years ago
10.1186/s12864-018-4559-3
ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq dataCited 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 cellsCited 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: almost 4 years ago
10.1016/j.devcel.2018.11.009
From Pioneer to Repressor: Bimodal foxd3 Activity Dynamically Remodels Neural Crest Regulatory Landscape In VivoCited 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 albicansCited by: 14
Author(s): Sabrina Jenull, Michael Tscherner, Theresia Mair, Karl Kuchler
Software Mentions: 9
Published: about 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 cellsCited 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 DataCited by: 15
Author(s): Mayur Divate, Edwin Cheung
Software Mentions: 7
Published: over 6 years ago
10.1186/s13059-020-02156-3
STARR-seq identifies active, chromatin-masked, and dormant enhancers in pluripotent mouse embryonic stem cellsCited 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 embryosCited by: 29
Author(s): Theodora Koromila, Fan Gao, Yohei Iwasaki, Peng He, Lior Pachter, J. Peter Gergen, Angelike Stathopoulos
Software Mentions: 7
Published: over 4 years ago
10.7554/eLife.28275
Concentration dependent chromatin states induced by the bicoid morphogen gradientCited 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 CHD4Cited by: 22
Author(s): Xiaoyun Sun, Wenjun Yu, Li Li, Yuhua Sun
Software Mentions: 6
Published: over 4 years ago
10.3389/fgene.2020.618478
ATACgraph: Profiling Genome-Wide Chromatin Accessibility From ATAC-seqCited 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: almost 4 years ago
10.7554/eLife.39911
A new experimental platform facilitates assessment of the transcriptional and chromatin landscapes of aging yeastCited 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: about 6 years ago
10.1038/s41598-018-33779-z
Chromatin accessibility landscape of articular knee cartilage reveals aberrant enhancer regulation in osteoarthritisCited 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: about 6 years ago
10.1038/s41598-019-41639-7
Hox gene expression determines cell fate of adult periosteal stem/progenitor cellsCited 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 embryogenesisCited 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 CellsCited by: 16
Author(s): Xiaoyin Shan, Cleresa Roberts, Yemin Lan, Ivona Percec
Software Mentions: 1
Published: over 6 years ago