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: HMMcopy
https://packages.ecosyste.ms/registries/bioconductor.org/packages/HMMcopy
Copy number prediction with correction for GC and mappability bias for HTS data
1 version
Latest release: about 1 year ago
1 dependent package
59,479 downloads total
Papers Mentioning HMMcopy 18
10.3389/fgene.2021.655536
Machine Intelligence in Single-Cell Data Analysis: Advances and New ChallengesCited by: 30
Author(s): Jiajia Li, Zusen Fan, Weiling Zhao, Xiaobo Zhou
Software Mentions: 12
Published: over 3 years ago
10.1186/s12864-021-07686-z
Evaluation of tools for identifying large copy number variations from ultra-low-coverage whole-genome sequencing dataCited by: 6
Author(s): Johannes Smolander, Sofia Khan, Kalaimathy Singaravelu, Leni Kauko, Riikka Lund, Asta Laiho, Laura L. Elo
Software Mentions: 6
Published: over 3 years ago
10.1371/journal.pcbi.1008012
Assessing the performance of methods for copy number aberration detection from single-cell DNA sequencing dataCited by: 24
Author(s): Xian Mallory, Mohammadamin Edrisi, Nicholas E. Navin, Luay Nakhleh
Software Mentions: 5
Published: over 4 years ago
10.3389/fgene.2020.505441
SCCNV: A Software Tool for Identifying Copy Number Variation From Single-Cell Whole-Genome SequencingCited by: 5
Author(s): Xiao Dong, Lei Zhang, Xiaoxiao Hao, Tao Wang, Jan Vijg
Software Mentions: 5
Published: about 4 years ago
10.1007/s13238-020-00728-4
SIRT7 antagonizes human stem cell aging as a heterochromatin stabilizerCited by: 69
Author(s): Shijia Bi, Zunpeng Liu, Zeming Wu, Zehua Wang, Xiaoqian Liu, Si Wang, Jie Ren, Yan Yao, Weiqi Zhang, Moshi Song, Guanghui Liu, Jing Qu
Software Mentions: 4
Published: over 4 years ago
10.1186/s13059-020-02119-8
Methods for copy number aberration detection from single-cell DNA-sequencing dataCited by: 63
Author(s): Xian Mallory, Mohammadamin Edrisi, Nicholas E. Navin, Luay Nakhleh
Software Mentions: 4
Published: over 4 years ago
10.1371/journal.pgen.1008558
Autophagy gene haploinsufficiency drives chromosome instability, increases migration, and promotes early ovarian tumorsCited by: 28
Author(s): Joe R. Delaney, C. A. Patel, Jaidev Bapat, Christian M. Jones, Maria Ramos-Zapatero, Katherine K. Ortell, Ralph Tanios, Mina Haghighiabyaneh, Joshua Axelrod, John W. DeStefano, Isabelle Tancioni, David D. Schlaepfer, Olivier Harismendy, Albert R. La Spada, Dwayne G. Stupack
Software Mentions: 4
Published: almost 5 years ago
10.1038/cr.2017.82
Single-cell multi-omics sequencing of mouse early embryos and embryonic stem cellsCited by: 262
Author(s): Fan Guo, Lin Li, Jingyun Li, Xinglong Wu, Boqiang Hu, Ping Zhu, Lu Wen, Fuchou Tang
Software Mentions: 4
Published: over 7 years ago
10.3389/fcell.2021.661272
Low-Coverage Whole Genome Sequencing of Cell-Free DNA From Immunosuppressed Cancer Patients Enables Tumor Fraction Determination and Reveals Relevant Copy Number AlterationsCited by: 5
Author(s): Amira Bouzidi, Karim Labreche, Marine Baron, Marianne Veyri, Jérôme Alexandre Denis, Mehdi Touat, Marc Sanson, Frédéric Davi, Erell Guillerm, Stéphanie Jouannet, F. Charlotte, Franck Bielle, Sylvain Choquet, Pierre‐Yves Boëlle, Jacques Cadranel, Véronique Leblond, Brigitte Autran, Jean–Marc Lacorte, Jean‐Philippe Spano, Florence Coulet
Software Mentions: 3
Published: over 3 years ago
10.1186/s40246-015-0044-0
Copy number alterations detected by whole-exome and whole-genome sequencing of esophageal adenocarcinomaCited by: 19
Author(s): Xiaoyu Wang, Xiaohong Li, Yu‐Shan Cheng, Xin Sun, Xibin Sun, Steven G. Self, Charles Kooperberg, James Y. Dai
Software Mentions: 2
Published: over 9 years ago
10.1186/s12864-016-2876-y
Comparative genomics and transcriptomics of Pichia pastorisCited by: 63
Author(s): Kerry R. Love, Kartik Shah, Charles A. Whittaker, Jie Wu, M. Catherine Bartlett, Duanduan Ma, Rachel Leeson, Margaret Priest, Jonathan Borowsky, Sarah Young, J. Christopher Love
Software Mentions: 2
Published: over 8 years ago
10.1038/s41375-019-0546-1
Cryptic genomic lesions in adverse-risk acute myeloid leukemia identified by integrated whole genome and transcriptome sequencingCited by: 12
Author(s): Jaeseung C. Kim, Philip C. Zuzarte, Tracy Murphy, Michelle Chan-Seng-Yue, Andrew Brown, Paul M. Krzyzanowski, Adam C. Smith, Faiyaz Notta, Mark D. Minden, John Douglas Mcpherson
Software Mentions: 2
Published: over 5 years ago
10.1371/journal.pbio.3000201
Up-regulation of FOXD1 by YAP alleviates senescence and osteoarthritisCited by: 91
Author(s): Ling Fu, Yuqiong Hu, Moshi Song, Zunpeng Liu, Weiqi Zhang, Fa-Xing Yu, Jun Wu, Si Wang, Juan Carlos Izpisúa Belmonte, Piu Chan, Jing Qu, Fuchou Tang, Guang Hui Liu
Software Mentions: 2
Published: almost 6 years ago
10.1007/s13238-019-0610-7
Telomere-dependent and telomere-independent roles of RAP1 in regulating human stem cell homeostasisCited by: 30
Author(s): Xing Zhang, Zunpeng Liu, Xiaoqian Liu, Si Wang, Yiyuan Zhang, Xiaojuan He, Shuhui Sun, Shuai Ma, Ng Shyh‐Chang, Feng Liu, Qiang Wang, Xiaoqun Wang, Lin Liu, Weiqi Zhang, Moshi Song, Guanghui Liu, Jing Qu
Software Mentions: 2
Published: almost 6 years ago
10.1038/s41598-017-16813-4
Comprehensive statistical inference of the clonal structure of cancer from multiple biopsiesCited by: 1
Author(s): Jie Liu, John T. Halloran, Jeffrey A. Bilmes, Riza M. Daza, Choli Lee, Elisabeth Mahen, Donna Prunkard, Chang Woo Song, Sibel Blau, Michael O. Dorschner, Vijayakrishna K. Gadi, Jay Shendure, C. Anthony Blau, William S. Noble
Software Mentions: 2
Published: about 7 years ago
10.1186/s12859-019-3266-7
A systematic evaluation of copy number alterations detection methods on real SNP array and deep sequencing dataCited by: 5
Author(s): Fei Luo
Software Mentions: 2
Published: about 5 years ago
10.1038/s41598-019-47489-7
Analysis of circulating cell-free DNA identifies KRAS copy number gain and mutation as a novel prognostic marker in Pancreatic cancerCited by: 34
Author(s): Sumitra Mohan, Mahmood Ayub, Dominic G. Rothwell, Sakshi Gulati, Bedirhan Kilerci, Antoine Hollebecque, Hui Sun Leong, Nigel Smith, Sudhakar Sahoo, Tine Descamps, Cong Zhou, Richard A Hubner, Mairéad G. McNamara, Ángela Lamarca, Juan W. Valle, Caroline Dive, Ged Brady
Software Mentions: 1
Published: over 5 years ago