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: CNAnorm
https://packages.ecosyste.ms/registries/bioconductor.org/packages/CNAnorm
A normalization method for Copy Number Aberration in cancer samples
1 version
Latest release: 10 months ago
25,401 downloads total
Papers Mentioning CNAnorm 21
10.1186/1471-2164-15-178
seqCNA: an R package for DNA copy number analysis in cancer using high-throughput sequencingCited by: 12
Author(s): David Mósen-Ansorena, Naiara Tellería, Silvia Veganzones, Virginia de la Orden, M.L. Maestro, Ana M. Aransay
Software Mentions: 7
Published: over 10 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: about 3 years ago
10.1128/mSphere.00167-17
Adaptive Mistranslation Accelerates the Evolution of Fluconazole Resistance and Induces Major Genomic and Gene Expression Alterations in Candida albicansCited by: 25
Author(s): Tobias Weil, Rodrigo Santamaría, Wanseon Lee, Johan Rung, Noemi Tocci, Darren Abbey, Ana R. Bezerra, Laura Carreto, Gabriela Moura, Mònica Bayés, Marta Gut, Attila Csikász‐Nagy, Duccio Cavalieri, Judith Berman, Manuel A. S. Santos
Software Mentions: 6
Published: almost 7 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: about 4 years ago
10.1186/1471-2105-14-S11-S1
Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectivesCited by: 426
Author(s): Min Zhao, Qingguo Wang, Quan Wang, Peilin Jia, Zhongming Zhao
Software Mentions: 5
Published: almost 11 years ago
10.1371/journal.pone.0078143
SomatiCA: Identifying, Characterizing and Quantifying Somatic Copy Number Aberrations from Cancer Genome Sequencing DataCited by: 28
Author(s): Mengjie Chen, Murat Günel, Hongyu Zhao
Software Mentions: 4
Published: over 10 years ago
10.1186/s13059-014-0443-x
SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritizationCited by: 58
Author(s): Yi Qiao, Aaron R. Quinlan, Amir A. Jazaeri, Roeland Verhaak, David A. Wheeler, Gábor Marth
Software Mentions: 3
Published: almost 10 years ago
10.1371/journal.pone.0059128
Comparative Studies of Copy Number Variation Detection Methods for Next-Generation Sequencing TechnologiesCited by: 133
Author(s): Junbo Duan, Jigang Zhang, Hong‐Wen Deng, Yuping Wang
Software Mentions: 3
Published: over 11 years ago
10.1186/s12864-019-5502-y
Identification and characterization of genes with absolute mRNA abundances changes in tumor cells with varied transcriptome sizesCited by: 2
Author(s): Hao Cai, Xiangyu Li, Jun He, Wenbin Zhou, Kai Song, You Guo, Huaping Liu, Qingzhou Guan, Haidan Yan, Xianlong Wang, Zheng Guo
Software Mentions: 3
Published: over 5 years ago
10.1093/gigascience/giaa118
CopyDetective: Detection threshold–aware copy number variant calling in whole-exome sequencing dataCited by: 5
Author(s): Sarah Sandmann, Marius Wöste, Aniek O. de Graaf, Birgit Burkhardt, Joop H. Jansen, Martin Dugas
Software Mentions: 3
Published: over 3 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: over 4 years ago
10.7717/peerj.836
GROM-RD: resolving genomic biases to improve read depth detection of copy number variantsCited by: 25
Author(s): Sean D. Smith, Joseph Kawash, Andrey Grigoriev
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.pcbi.1004618
SAAS-CNV: A Joint Segmentation Approach on Aggregated and Allele Specific Signals for the Identification of Somatic Copy Number Alterations with Next-Generation Sequencing DataCited by: 34
Author(s): Zhongyang Zhang, Ke Hao
Software Mentions: 2
Published: over 8 years ago
10.3389/fgene.2020.569227
RKDOSCNV: A Local Kernel Density-Based Approach to the Detection of Copy Number Variations by Using Next-Generation Sequencing DataCited by: 5
Author(s): Guojun Liu, Junying Zhang, Xiguo Yuan, Chao Wei
Software Mentions: 2
Published: over 3 years ago
10.3389/fgene.2021.700874
CNV-MEANN: A Neural Network and Mind Evolutionary Algorithm-Based Detection of Copy Number Variations From Next-Generation Sequencing DataCited by: 7
Author(s): Tihao Huang, Junqing Li, Baoxian Jia, Hongshi Sang
Software Mentions: 2
Published: almost 3 years ago
10.1186/s13073-017-0442-0
The genomic road to invasion—examining the similarities and differences in the genomes of associated oral pre-cancer and cancer samplesCited by: 30
Author(s): Henry M. Wood, Catherine Daly, Rebecca Chalkley, Burcu Şengüven, Lisa Ross, Philip Egan, Preetha Chengot, Jennifer Graham, Neeraj Sethi, T.K. Ong, Kenneth MacLennan, Pamela Rabbitts, Caroline Conway
Software Mentions: 2
Published: about 7 years ago
10.1038/srep44700
Establishment of a novel cellular model for myxofibrosarcoma heterogeneityCited by: 16
Author(s): Birgit Lohberger, Nicole Stuendl, Andreas Leithner, Beate Rinner, Stefan Sauer, Karl Kashofer, Bernadette Liegl‐Atzwanger
Software Mentions: 2
Published: over 7 years ago
10.1186/s12859-018-2099-0
Modeling and correct the GC bias of tumor and normal WGS data for SCNA based tumor subclonal population inferringCited by: 2
Author(s): Yanshuo Chu, Mingxiang Teng, Yadong Wang
Software Mentions: 1
Published: over 6 years ago
10.1186/1471-2164-15-251
Copy number variations among silkwormsCited by: 10
Author(s): Qian Zhao, Minjin Han, Wei Sun, Ze Zhang
Software Mentions: 1
Published: over 10 years ago
10.1186/gb-2013-14-7-r80
THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing dataCited by: 218
Author(s): Layla Oesper, Ahmad Mahmoody, Benjamin J. Raphael
Software Mentions: 1
Published: over 11 years ago
10.1186/s12859-020-03859-x
Performance of copy number variants detection based on whole-genome sequencing by DNBSEQ platformsCited by: 8
Author(s): Junhua Rao, Lihua Peng, Xinming Liang, Hui Jiang, Chunyu Geng, Xing‐Ming Zhao, Xin Liu, Guangyi Fan, Fang Chen, Feng Mu
Software Mentions: 1
Published: over 3 years ago