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: CopywriteR
https://packages.ecosyste.ms/registries/bioconductor.org/packages/CopywriteR
Copy number information from targeted sequencing using off-target reads
1 version
Latest release: about 1 year ago
18,346 downloads total
Papers Mentioning CopywriteR 28
10.1016/j.cell.2016.08.041
A Biobank of Breast Cancer Explants with Preserved Intra-tumor Heterogeneity to Screen Anticancer CompoundsCited by: 359
Author(s): Alejandra Bruna, Oscar M. Rueda, Wendy Greenwood, Ankita Batra, Maurizio Callari, R N Batra, Katherine Pogrebniak, José Luís Sandoval, John W. Cassidy, Ana Tufegdžić Vidaković, Stephen‐John Sammut, Linda Jones, Elena Provenzano, Richard D. Baird, Peter Eirew, James Hadfield, Matthew Eldridge, Anne McLaren-Douglas, Andrew Barthorpe, Howard Lightfoot, Mark J. O’Connor, Joe W. Gray, Javier Cortés, José Baselga, Elisabetta Marangoni, Alana L. Welm, Samuel Aparicio, Violeta Serra, Mathew J. Garnett, Carlos Caldas
Software Mentions: 11
Published: about 8 years ago
10.1186/s13059-021-02316-z
A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequencyCited by: 24
Author(s): Wendell Jones, Binsheng Gong, Natalia Novoradovskaya, Dan Li, Rebecca Kusko, Todd Richmond, Donald J. Johann, Halil Bişğin, Sayed Mohammad Ebrahim Sahraeian, Pierre R. Bushel, Mehdi Pirooznia, Katherine Wilkins, Marco Chierici, Wenjun Bao, Lee S Basehore, Anne Bergstrom Lucas, Daniel L. Burgess, Daniel Butler, Simon Cawley, Chia Jung Chang, Guangchun Chen, Tao Chen, Yun Ching Chen, Daniel J. Craig, Ángela del Pozo, Jonathan Foox, Margherita Francescatto, Yutao Fu, Cesare Furlanello, Kristina Giorda, Kira P. Grist, Meijian Guan, You-Zeng Hao, Scott Happe, Gunjan Hariani, Nathan Haseley, Jeff S. Jasper, Giuseppe Jurman, David P. Kreil, Paweł P. Łabaj, Kevin Lai, Jianying Li, Quan Zhen Li, Yulong Li, Chi Kong Li, Zhichao Liu, Mario Solís-López, Kelci Miclaus, Raymond D. Miller, Vinay Kumar Mittal, Marghoob Mohiyuddin, Carlos Pabón-Peña, Barbara L. Parsons, Fujun Qiu, Andreas Scherer, Tieliu Shi, Suzy M. Stiegelmeyer, Chen Suo, Nikola Tom, Dong Wang, Zhining Wen, Leihong Wu, Wenzhong Xiao, Chang Xu, Ying Yu, Jiyang Zhang, Yifan Zhang, Zhihong Zhang, Yuanting Zheng, Christopher E. Mason, James C. Willey, Leming Shi, Joshua Xu
Software Mentions: 10
Published: over 3 years ago
10.1371/journal.pcbi.1004873
CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA SequencingCited by: 1,141
Author(s): Eric Talevich, A. Hunter Shain, Thomas Botton, Boris C. Bastian
Software Mentions: 9
Published: over 8 years ago
10.1093/bib/bbx143
Bioinformatics for precision oncologyCited by: 49
Author(s): Jochen Singer, Anja Irmisch, Hans‐Joachim Ruscheweyh, Franziska Singer, Nora C. Toussaint, Mitchell P. Levesque, Daniel J. Stekhoven, Niko Beerenwinkel
Software Mentions: 7
Published: almost 7 years ago
10.1038/s41598-021-85256-9
Creation and validation of models to predict response to primary treatment in serous ovarian cancerCited by: 11
Author(s): Jesús González Bosquet, Eric J. Devor, A.M. Newtson, Brian J. Smith, David Bender, Michael J. Goodheart, Megan McDonald, Terry A. Braun, Kristina W. Thiel, Kimberly K. Leslie
Software Mentions: 6
Published: over 3 years ago
10.1186/s13059-020-02188-9
Convergent network effects along the axis of gene expression during prostate cancer progressionCited by: 14
Author(s): Konstantina Charmpi, Tiannan Guo, Qing Zhong, Ulrich Wagner, Rui Sun, Nora C. Toussaint, Christine Fritz, Chunhui Yuan, Hao Chen, Niels J. Rupp, Ailsa J. Christiansen, Dorothea Rutishauser, Jan H. Rüschoff, Christian Daniel Fankhauser, Karim Saba, Cédric Poyet, Thomas Hermanns, Kathrin Oehl, Ariane L. Moore, Christian Beisel, Laurence Calzone, Loredana Martignetti, Qiushi Zhang, Yi Zhu, María Rodríguez Martínez, Matteo Manica, Michael C. Haffner, Ruedi Aebersold, Peter J. Wild, Andreas Beyer
Software Mentions: 5
Published: almost 4 years ago
10.1016/j.cell.2017.07.025
Heterogeneous Tumor-Immune Microenvironments among Differentially Growing Metastases in an Ovarian Cancer PatientCited by: 338
Author(s): Alejandro Jiménez-Sánchez, Danish Memon, Stephane Pourpe, Harini Veeraraghavan, Yanyun Li, Hebert Alberto Vargas, Michael B. Gill, Kay J. Park, Oliver Zivanovic, Jason Konner, Jacob Ricca, Dmitriy Zamarin, Tyler Walther, Carol Aghajanian, Jedd D. Wolchok, Evis Sala, Taha Merghoub, Alexandra Snyder, Martin L. Miller
Software Mentions: 5
Published: over 7 years ago
10.1084/jem.20191257
Combined deletion of <i>Bap1</i>, <i>Nf2</i>, and <i>Cdkn2ab</i> causes rapid onset of malignant mesothelioma in miceCited by: 28
Author(s): Jitendra Badhai, Gaurav Kumar Pandey, Ji‐Ying Song, Oscar Krijgsman, Rajith Bhaskaran, G. Chandrasekaran, Min-Chul Kwon, Lorenzo Bombardelli, Kim Monkhorst, Cristoforo Grasso, John Zevenhoven, Jan van der Vliet, Miranda Cozijnsen, Paul Krimpenfort, Daniel S. Peeper, Maarten van Lohuizen, Anton Berns
Software Mentions: 5
Published: over 4 years ago
10.7554/eLife.50267
CNApp, a tool for the quantification of copy number alterations and integrative analysis revealing clinical implicationsCited by: 42
Author(s): Sebastià Franch‐Expósito, Laia Bassaganyas, María Vila-Casadesús, Eva Hernández‐Illán, Roger Esteban-Fabró, Marcos Díaz‐Gay, Juan José Lozano, Antoni Castells, Josep M. Llovet, Sergi Castellví–Bel, Jordi Camps
Software Mentions: 4
Published: almost 5 years ago
10.1242/dmm.049044
Comparison of the oncogenomic landscape of canine and feline hemangiosarcoma shows novel parallels with human angiosarcomaCited by: 16
Author(s): Kim Wong, Latasha Ludwig, Oscar Krijgsman, David J. Adams, Geoffrey A. Wood, Louise van der Weyden
Software Mentions: 4
Published: over 3 years ago
10.1186/s13059-015-0617-1
CopywriteR: DNA copy number detection from off-target sequence dataCited by: 169
Author(s): Thomas Kuilman, Arno Velds, Kristel Kemper, Marco Ranzani, Lorenzo Bombardelli, Marlous Hoogstraat, Ekaterina Nevedomskaya, Guotai Xu, Julian de Ruiter, Martijn P. Lolkema, Bauke Ylstra, Jos Jonkers, Sven Rottenberg, Lodewyk F.A. Wessels, David J. Adams, Daniel S. Peeper, Oscar Krijgsman
Software Mentions: 4
Published: over 9 years ago
10.1186/s12920-018-0320-7
Efficient strategy for the molecular diagnosis of intractable early-onset epilepsy using targeted gene sequencingCited by: 41
Author(s): John Hoon Rim, Se Hee Kim, In Sik Hwang, Soon Sung Kwon, Jieun Kim, Hyun Woo Kim, Min Jung Cho, Ara Ko, Song Ee Youn, Kim Ji-Hun, Young Mock Lee, Hee Jung Chung, Joon Soo Lee, Heung Dong Kim, Jong Rak Choi, Seung Tae Lee, Hoon Chul Kang
Software Mentions: 4
Published: almost 7 years ago
10.3390/ijms20051205
A Prediction Model for Preoperative Risk Assessment in Endometrial Cancer Utilizing Clinical and Molecular VariablesCited by: 12
Author(s): E. Salinas, M.D. Miller, A.M. Newtson, Deepti Sharma, Megan McDonald, Matthew E. Keeney, Brian J. Smith, David Bender, Michael J. Goodheart, Kristina W. Thiel, Eric J. Devor, Kimberly K. Leslie, Jesús González Bosquet
Software Mentions: 3
Published: over 5 years ago
10.1038/s41416-020-0797-7
The prognostic significance of immune microenvironment in breast ductal carcinoma in situCited by: 25
Author(s): Michael S. Toss, Asima Abidi, Dorothea Lesche, Chitra Joseph, Sakshi Mahale, Hugo Saunders, Tanjina Kader, Islam M. Miligy, Andrew Green, Kylie L. Gorringe, Emad A. Rakha
Software Mentions: 3
Published: over 4 years ago
10.20892/j.issn.2095-3941.2020.0012
Patient-derived non-small cell lung cancer xenograft mirrors complex tumor heterogeneityCited by: 15
Author(s): Xuanming Chen, Cheng Shen, Zhe Wei, Rui Zhang, Yongsheng Wang, Lili Jiang, Ke Chen, Shuang Qiu, Yuanli Zhang, Ting Zhang, Bin Chen, Yanjun Xu, Qiyi Feng, Jen‐Wei Huang, Zhihui Zhong, Hongxia Li, Guowei Che, Kai Xiao
Software Mentions: 3
Published: almost 4 years ago
10.1371/journal.pgen.1008960
Interplay between UNG and AID governs intratumoral heterogeneity in mature B cell lymphomaCited by: 3
Author(s): Pilar Delgado, Ángel F. Álvarez-Prado, Ester Marina-Zárate, Isora V. Sernández, Sonia M. Mur, Jorge de la Barrera, Fátima Sánchez-Cabo, Marta Cañamero, Antonio Molina, Laura Belver, Virginia G. de Yébenes, Almudena R. Ramiro
Software Mentions: 3
Published: almost 4 years ago
10.15252/emmm.201911756
Cancer of Unknown Primary ( <scp>CUP</scp> ): genetic evidence for a novel nosological entity? A case reportCited by: 8
Author(s): Silvia Benvenuti, Melissa Milan, Elena Geuna, Alberto Pisacane, Rebecca Senetta, Gennaro Gambardella, Giulia Maria Stella, Filippo Montemurro, Anna Sapino, Carla Boccaccio, Paolo M. Comoglio
Software Mentions: 3
Published: over 4 years ago
10.1186/s12859-020-3397-x
CNV Radar: an improved method for somatic copy number alteration characterization in oncologyCited by: 8
Author(s): David Soong, Jeran K. Stratford, Hervé Avet‐Loiseau, Nizar J. Bahlis, Faith E. Davies, Angela Dispenzieri, A. Kate Sasser, Jordan M. Schecter, Ming Qi, Chad Brown, Wendell Jones, Jonathan J. Keats, Daniel Auclair, Christopher Chiu, Jason Powers, Michael Schäffer
Software Mentions: 3
Published: over 4 years ago
10.1186/s12864-016-3074-7
CNARA: reliability assessment for genomic copy number profilesCited by: 4
Author(s): Ai Ni, Haoyang Cai, Caius Solovan, Michael Baudis
Software Mentions: 2
Published: about 8 years ago
10.1186/s13058-020-01328-0
Clinical implications of prospective genomic profiling of metastatic breast cancer patientsCited by: 29
Author(s): Courtney T. van Geelen, Peter Savas, Zhi L. Teo, Stephen J. Luen, Chen-Fang Weng, Yi-An Ko, Keilly Kuykhoven, Franco Caramia, Roberto Salgado, Prudence A. Francis, Sarah-Jane Dawson, Stephen B. Fox, Andrew Fellowes, Sherene Loi
Software Mentions: 2
Published: over 4 years ago
10.3390/biology10070584
CIRCNV: Detection of CNVs Based on a Circular Profile of Read Depth from Sequencing DataCited by: 1
Author(s): Huijing Zhao, Qi Li, Yuan Tian, Yuehui Chen, Haque A.K. Alvi, Xiguo Yuan
Software Mentions: 2
Published: over 3 years ago
10.1101/mcs.a001495
<i>FGFR2</i> amplification in colorectal adenocarcinomaCited by: 18
Author(s): Jamal Carter, Catherine E. Cottrell, Samantha N. McNulty, Katinka A. Vigh‐Conrad, Stephen Lamp, Jonathan W. Heusel, Eric J. Duncavage
Software Mentions: 2
Published: about 7 years ago
10.3389/fgene.2020.632311
A Density Peak-Based Method to Detect Copy Number Variations From Next-Generation Sequencing DataCited by: 2
Author(s): Kai Xie, Yuan Tian, Xiguo Yuan
Software Mentions: 2
Published: almost 4 years ago
10.1371/journal.pone.0212228
Targeted next generation sequencing can serve as an alternative to conventional tests in myeloid neoplasmsCited by: 10
Author(s): Borahm Kim, Hyeonah Lee, Ji Eun Jang, Soo Jeong Kim, Seung Tae Lee, June Won Cheong, Chuhl Joo Lyu, Yoo Hong Min, Jong Rak Choi
Software Mentions: 2
Published: over 5 years ago
10.1002/1878-0261.12817
Tumor and germline next generation sequencing in high grade serous cancer: experience from a large population‐based testing programCited by: 12
Author(s): Melanie Care, Jeanna McCuaig, Blaise Clarke, Sylvie Grenier, Raymond H. Kim, Marjan Rouzbahman, Natalie Stickle, Marcus Q. Bernardini, Tracy L. Stockley
Software Mentions: 2
Published: about 4 years ago
10.15252/emmm.201404914
Intra‐ and inter‐tumor heterogeneity in a vemurafenib‐resistant melanoma patient and derived xenograftsCited by: 123
Author(s): Kristel Kemper, Oscar Krijgsman, Paulien Cornelissen-Steijger, Aida Shahrabi, Fleur Weeber, Ji‐Ying Song, Thomas Kuilman, Daniël J. Vis, Lodewyk Wessels, Emile E. Voest, Ton N. Schumacher, Christian U. Blank, David J. Adams, John B.A.G. Haanen, Daniel S. Peeper
Software Mentions: 1
Published: over 9 years ago
10.3390/cancers13112742
Whole Exome Sequencing of Biliary Tubulopapillary Neoplasms Reveals Common Mutations in Chromatin Remodeling GenesCited by: 8
Author(s): Claudia Groß, Thomas Engleitner, Sebastian Lange, Julia Weber, Moritz Jesinghaus, Björn Konukiewitz, Alexander Muckenhuber, Katja Steiger, Nicole Pfarr, Benjamin Goeppert, Gisela Keller, Wilko Weichert, N. Volkan Adsay, Günter Klöppel, Roland Rad, Irene Espósito, Anna Melissa Schlitter
Software Mentions: 1
Published: over 3 years ago
10.1371/journal.pone.0194472
Xome-Blender: A novel cancer genome simulatorCited by: 14
Author(s): Roberto Semeraro, Valerio Orlandini, Alberto Magi
Software Mentions: 1
Published: over 6 years ago