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: pyDNase

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

DNase-seq analysis library
17 versions
Latest release: over 6 years ago
330 downloads last month

Papers Mentioning pyDNase 12

Interactions between lineage‐associated transcription factors govern haematopoietic progenitor states
Cited by: 17
Author(s): Iwo Kuciński, Nicola K. Wilson, Rebecca Hannah, Sarah Kinston, Pierre Cauchy, Aurelie Lenaerts, Rudolf Grosschedl, Berthold Göttgens
Software Mentions: 9
Published: about 4 years ago

10.1186/s13059-020-02082-4

Genome-wide studies reveal the essential and opposite roles of ARID1A in controlling human cardiogenesis and neurogenesis from pluripotent stem cells
Cited by: 22
Author(s): Juli Liu, Sheng Liu, Hongyu Gao, Lei Han, Xun Chu, Sheng Yi, Weinian Shou, Yue Wang, Yunlong Liu, Jun Wan, Lei Yang
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pgen.1008265

Genome-wide discovery of the daily transcriptome, DNA regulatory elements and transcription factor occupancy in the monarch butterfly brain
Cited by: 23
Author(s): Aldrin B. Lugena, Ying Zhang, Jérôme S. Menet, Christine Merlin
Software Mentions: 7
Published: over 5 years ago

10.1155/2021/8880585

Gene Regulatory Network of Human GM-CSF-Secreting T Helper Cells
Cited by: 3
Author(s): Szabolcs Éliás, Angelika Schmidt, David Green, Jesper Tegnér
Software Mentions: 5
Published: over 3 years ago

10.1186/s12864-018-4943-z

ATAC2GRN: optimized ATAC-seq and DNase1-seq pipelines for rapid and accurate genome regulatory network inference
Cited by: 19
Author(s): Thomas Pranzatelli, Drew G. Michael, John A. Chiorini
Software Mentions: 5
Published: over 6 years ago

10.1016/j.celrep.2020.107748

Chromatin Priming Renders T Cell Tolerance-Associated Genes Sensitive to Activation below the Signaling Threshold for Immune Response Genes
Cited by: 20
Author(s): Sarah L Bevington, Sky T. H. Ng, Graham J. Britton, Peter Keane, David C. Wraith, Peter N. Cockerill
Software Mentions: 4
Published: over 4 years ago

10.1186/s12859-017-1769-7

Assessing the model transferability for prediction of transcription factor binding sites based on chromatin accessibility
Cited by: 21
Author(s): Sheng Liu, Cristina Zibetti, Jun Wan, Guohua Wang, Seth Blackshaw, Jiang Qian
Software Mentions: 3
Published: over 7 years ago

10.1186/s12915-021-01114-0

Profiling of chromatin accessibility identifies transcription factor binding sites across the genome of Aspergillus species
Cited by: 7
Author(s): Lianggang Huang, Xuejie Li, Lü Dong, Bin Wang, Li Pan
Software Mentions: 3
Published: about 3 years ago

10.1186/s12864-015-2081-4

Wellington-bootstrap: differential DNase-seq footprinting identifies cell-type determining transcription factors
Cited by: 50
Author(s): Jason Piper, Salam A. Assi, Pierre Cauchy, Christophe Ladroue, Peter N. Cockerill, Constanze Bonifer, Sascha Ott
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-021-88003-2

Scrt1, a transcriptional regulator of β-cell proliferation identified by differential chromatin accessibility during islet maturation
Cited by: 5
Author(s): Jonathan Sobel, Claudiane Guay, Ofer Elhanani, Adriana Rodríguez-Trejo, Lisa Stoll, Véronique Menoud, Cécile Jacovetti, Michael D. Walker, Romano Regazzi
Software Mentions: 3
Published: over 3 years ago

10.1038/s42003-020-01403-4

ATAC-seq with unique molecular identifiers improves quantification and footprinting
Cited by: 15
Author(s): Tao Zhu, Keyan Liao, Rongfang Zhou, Chen Xia, Weibo Xie
Software Mentions: 2
Published: almost 4 years ago

10.3389/fimmu.2021.642807

Stable Epigenetic Programming of Effector and Central Memory CD4 T Cells Occurs Within 7 Days of Antigen Exposure In Vivo
Cited by: 3
Author(s): Sarah L Bevington, Rémi Fiancette, Dominika W Gajdasik, Peter Keane, Jake K Soley, Claire Willis, Dan Coleman, David R. Withers, Peter N. Cockerill
Software Mentions: 2
Published: over 3 years ago