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: PureCN
https://packages.ecosyste.ms/registries/bioconductor.org/packages/PureCN
Copy number calling and SNV classification using targeted short read sequencing
1 version
Latest release: about 1 year ago
23,253 downloads total
Papers Mentioning PureCN 11
10.1016/j.cell.2019.10.007
Integrated Proteogenomic Characterization of Clear Cell Renal Cell CarcinomaCited by: 375
Author(s): David Clark, Saravana M. Dhanasekaran, Francesca Petralia, Jianbo Pan, Xiaoyu Song, Yingwei Hu, Felipe da Veiga Leprevost, Boris Reva, Tung-Shing Mamie Lih, Hui-Yin Chang, Wanli Ma, Chen Huang, Christopher J. Ricketts, Lijun Chen, Azra Krek, Yize Li, Dmitry Rykunov, Qing Kay Li, Lin S. Chen, Umut Özbek, Suhas Vasaikar, Yige Wu, Seungyeul Yoo, Shrabanti Chowdhury, Matthew A. Wyczalkowski, Jiayi Ji, Michael Schnaubelt, Andy T. Kong, Sunantha Sethuraman, Dmitry M. Avtonomov, Minghui Ao, Antonio Colaprico, Song Cao, Kyung-Cho Cho, Selim Kalayci, Shiyong Ma, Wenke Liu, Kelly V. Ruggles, Anna Calinawan, Zeynep H. Gümüş, Daniel Geiszler, Emily Kawaler, Guo Ci Teo, Bo Wen, Yuping Zhang, Sarah Keegan, Kai Li, Feng Chen, Nathan Edwards, Phillip M. Pierorazio, Xi Steven Chen, Christian P. Pavlovich, A. Ari Hakimi, Gabriel Bromiński, James J. Hsieh, Andrzej Antczak, Tatiana Omelchenko, Jan Lubiński, Maciej Wiznerowicz, W. Marston Linehan, Christopher R. Kinsinger, Mathangi Thiagarajan, Emily S. Boja, Mehdi Mesri, Tara Hiltke, Ana I. Robles, Henry Rodriguez, Jiang Qian, David Fenyö, Bing Zhang, Ding Li, Eric E. Schadt, Arul M. Chinnaiyan, Zhen Zhang, Gilbert S. Omenn, Marcin Cieślik, Daniel W. Chan, Alexey I. Nesvizhskii, Pei Wang, Hui Zhang, A. Samad Hashimi, Alexander Pico, Alla Karpova, Alyssa Charamut, Amanda G. Paulovich, Amy M. Perou, Anna Malovannaya, Annette Marrero-Oliveras, Anupriya Agarwal, Barbara Hindenach, Barbara L. Pruetz, Beom-Jun Kim, Brian J. Druker, Chelsea J. Newton, Chet Birger, Corbin D. Jones, Cristina E. Tognon, D. R. Mani, Dana R. Valley, Daniel C. Rohrer, Daniel Cui Zhou, Darlene Tansil, David Chesla, David I. Heiman, David A. Wheeler, Donghui Tan, Doug W. Chan, Emek Demir, Ewa Malc, Francesmary Modugno, Gaddy Getz, Galen Hostetter, George Wilson, Gerald W. Hart, Heng Zhu, Hongwei Liu, Houston Culpepper, Hua Sun, Hua Zhou, Jacob Day, James Suh, Jasmine Huang, Jason McDermott, Jeffrey R. Whiteaker, Jeffrey W. Tyner, Jennifer Eschbacher, Jin Chen, John P. McGee, Jun Zhu, Karen A. Ketchum, Karin D. Rodland, Karl R. Clauser, Karna Robinson, Karsten Krug, Katherine A. Hoadley, Ki Sung Um, Kim Elburn, Kimberly Holloway, Liang-Bo Wang, Lili M. Blumenberg, Linda Hannick, Liqun Qi, Lori J. Sokoll, MacIntosh Cornwell, Marc Loriaux, Marcin J. Domagalski, Marina Gritsenko, Matthew L. Anderson, Matthew E. Monroe, Matthew J. Ellis, Maureen A. Dyer, Meenakshi Anurag, Meghan C. Burke, Melissa Borucki, Michael A. Gillette, Michael J. Birrer, Michael R. Lewis, Michael Ittmann, Michael J. Smith, Michael Vernon, Michelle Chaikin, Milan G. Chheda, Munziba Khan, Nancy Roche, Nathan Edwards, Negin Vatanian, Nicole Tignor, Noam D. Beckmann, Pamela Grady, Patricia Castro, Paul Piehowski, Peter B. McGarvey, Piotr A. Mieczkowski, Pushpa Hariharan, Qingsong Gao, Rajiv Dhir, Ramani B. Kothadia, Ratna R. Thangudu, Rebecca Montgomery, Reyka G. Jayasinghe, Richard Smith, Robert A. Edwards, Robert Zelt, Ross M. Bremner, Ruiyang Liu, Runyu Hong, Sailaja Mareedu, Samuel H. Payne, Sandra Cottingham, Sanford P. Markey, Scott D. Jewell, Shalin Patel, Shankha Satpathy, Shannon Richey, Sherri R. Davies, Shuang Cai, Simina M. Boca, Snehal Patil, Sohini Sengupta, Sonya Carter, Stacey Gabriel, Stefani N. Thomas, Stephanie Young, Stephen E. Stein, Steven A. Carr, Steven M. Foltz, S. G. Hilsenbeck, Tanya Krubit, Tao Liu, Tara Skelly, Thomas F. Westbrook, Uma Borate, Uma Velvulou, Vladislav Petyuk, William Bocik, Xi Chen, Yan Shi, Yifat Geffen, Yihao Lu, Ying Wang, Yosef E. Maruvka, Zhi Li, Zhiao Shi, Zhidong Tu
Software Mentions: 10
Published: over 5 years ago
10.1371/journal.pgen.1009201
Genomic and transcriptomic landscape of conjunctival melanomaCited by: 14
Author(s): Katarina Cisarova, Marc Folcher, Ikram El Zaoui, Rosanna Pescini Gobert, Virginie G. Peter, Béryl Royer‐Bertrand, Léonidas Zografos, Ann Schalenbourg, Michaël Nicolas, Donata Rimoldi, Serge Leyvraz, Nicolò Riggi, Alexandre Moulin, Carlo Rivolta
Software Mentions: 7
Published: about 4 years ago
10.1371/journal.pcbi.1007603
SuperFreq: Integrated mutation detection and clonal tracking in cancerCited by: 34
Author(s): Christoffer Flensburg, Tobias Sargeant, Alicia Oshlack, Ian J. Majewski
Software Mentions: 4
Published: almost 5 years ago
10.1038/s12276-021-00583-1
High prevalence of TP53 loss and whole-genome doubling in early-onset colorectal cancerCited by: 11
Author(s): Jeong Eun Kim, Jaeyong Choi, Chang Ohk Sung, Yong Sang Hong, Sun Young Kim, Hyunjung Lee, Tae Won Kim, Jong‐Il Kim
Software Mentions: 4
Published: almost 4 years ago
10.1038/s41598-019-50805-w
Identification of somatic alterations in lipoma using whole exome sequencingCited by: 4
Author(s): Deepika Kanojia, Pushkar Dakle, Anand Mayakonda, Rajeev Parameswaran, Mark E. Puhaindran, Victor Kwan Min Lee, Vikas Madan, Phillip Koeffler
Software Mentions: 3
Published: about 5 years ago
10.1186/s13029-016-0060-z
PureCN: copy number calling and SNV classification using targeted short read sequencingCited by: 89
Author(s): Markus Riester, Angad Singh, A. Rose Brannon, Kun Yu, Catarina D. Campbell, Derek Y. Chiang, Michael Morrissey
Software Mentions: 2
Published: about 8 years ago
10.3389/fonc.2019.00119
Leveraging Spatial Variation in Tumor Purity for Improved Somatic Variant Calling of Archival Tumor Only SamplesCited by: 15
Author(s): Rebecca F. Halperin, Winnie S. Liang, Sidharth Kulkarni, Erica E. Tassone, Jonathan Adkins, Daniel Enríquez, Nhan L. Tran, Nicole C. Hank, James Newell, Chinnappa D. Kodira, Ronald L. Korn, Michael E. Berens, Kim S, Sara A. Byron
Software Mentions: 2
Published: almost 6 years ago
10.1136/jitc-2020-001199
Clinical advantage of targeted sequencing for unbiased tumor mutational burden estimation in samples with low tumor purityCited by: 4
Author(s): Tae Hee Hong, Hongui Cha, Joon Ho Shim, Boram Lee, Jongsuk Chung, Chung Lee, Nayoung K.D. Kim, Yoon‐La Choi, Soohyun Hwang, Yoomi Lee, Sehhoon Park, Hyun Ae Jung, Jiyeon Kim, Jong‐Mu Sun, Jin Seok Ahn, Myung‐Ju Ahn, Keunchil Park, Se‐Hoon Lee, Woong-Yang Park
Software Mentions: 1
Published: over 4 years ago
10.1371/journal.pone.0206632
Role of variant allele fraction and rare SNP filtering to improve cellular DNA repair endpoint associationCited by: 2
Author(s): David M. Vossen, Caroline V.M. Verhagen, Reidar Grénman, Roelof J.C. Kluin, Marcel Verheij, Michiel W. M. van den Brekel, Lodewyk Wessels, Conchita Vens
Software Mentions: 1
Published: about 6 years ago
10.3390/cancers11040445
Genetic Factors Associated with a Poor Outcome in Head and Neck Cancer Patients Receiving Definitive ChemoradiotherapyCited by: 15
Author(s): David M. Vossen, Caroline V.M. Verhagen, Martijn van der Heijden, Paul Essers, Harry Bartelink, Marcel Verheij, Lodewyk F.A. Wessels, Michiel W. M. van den Brekel, Conchita Vens
Software Mentions: 1
Published: almost 6 years ago
10.1038/s41419-021-03754-0
Distinct mutational backgrounds and clonal architectures implicated prognostic discrepancies in small-cell carcinomas of the esophagus and lungCited by: 0
Author(s): Zhengbo Song, Yueping Liu, Guoping Cheng, Lianpeng Chang, Zicheng Yu, Ming Chen, Gang Chen
Software Mentions: 1
Published: over 3 years ago