:: DESCRIPTION
SCYN is a CNV (Copy number variation) segmentation method powered with dynamic programming. SCYN resolves the precise segmentation on in silico dataset.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Feng X, Chen L, Qing Y, Li R, Li C, Li SC.
SCYN: single cell CNV profiling method using dynamic programming.
BMC Genomics. 2021 Nov 16;22(Suppl 5):651. doi: 10.1186/s12864-021-07941-3. PMID: 34789142.
:: DESCRIPTION
CNV Workshop is a web-enabled platform for analyzing genome variation such as copy number variation (CNV).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2010 Feb 4;11:74. doi: 10.1186/1471-2105-11-74.
CNV Workshop: an integrated platform for high-throughput copy number variation discovery and clinical diagnostics.
Gai X1, Perin JC, Murphy K, O’Hara R, D’arcy M, Wenocur A, Xie HM, Rappaport EF, Shaikh TH, White PS.
:: DESCRIPTION
EXCAVATOR is a novel software package for the detection and classification of genomic regions involved in copy numner variants that uses whole-exome sequencing data generated by second generation sequencing technologies.
EXCAVATOR2 is a collection of bash, R and Fortran scripts and codes that analyses Whole Exome Sequencing (WES) data to identify CNVs. EXCAVATOR2 enhances the identification of all genomic CNVs, both overlapping and non-overlapping targeted exons by integrating the analysis of In-targets and Off- targets reads.
XCAVATOR is a novel software package for the identification of genomic regions involved in copy number variants/alterations (CNVs/CNAs) from short and long reads whole-genome sequencing experiments.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Magi A, Pippucci T, Sidore C.
XCAVATOR: accurate detection and genotyping of copy number variants from second and third generation whole-genome sequencing experiments.
BMC Genomics. 2017 Sep 21;18(1):747. doi: 10.1186/s12864-017-4137-0. PMID: 28934930; PMCID: PMC5609061.
D’Aurizio R, Pippucci T, Tattini L, Giusti B, Pellegrini M, Magi A.
Enhanced copy number variants detection from whole-exome sequencing data using EXCAVATOR2.
Nucleic Acids Res. 2016 Nov 16;44(20):e154. doi: 10.1093/nar/gkw695. Epub 2016 Aug 9. PMID: 27507884; PMCID: PMC5175347.
Genome Biol. 2013;14(10):R120.
EXCAVATOR: detecting copy number variants from whole-exome sequencing data.
Magi A, Tattini L, Cifola I, D’Aurizio R, Benelli M, Mangano E, Battaglia C, Bonora E, Kurg A, Seri M, Magini P, Giusti B, Romeo G, Pippucci T, De Bellis G, Abbate R, Gensini GF.
:: DESCRIPTION
cnvCSEM (CNV: -guided C: hIP-S: eq by E: xpectation-M: aximization algorithm), is a flexible framework that incorporates CNV in multi-read allocation.
::DEVELOPER
Qi Zhang (qizhang at stat dot wisc dot edu)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: MORE INFORMATION
Citation
CNV-guided Multi-read Allocation for ChIP-seq.
Zhang Q, Keleş S.
Bioinformatics. 2014 Jun 24. pii: btu402.
:: DESCRIPTION
CNVannotator is a web server that accepts an input set of human genomic positions in a user-friendly tabular format.
::DEVELOPER
Bioinformatics and Systems Medicine Laboratory,
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
PLoS One. 2013 Nov 14;8(11):e80170. doi: 10.1371/journal.pone.0080170. eCollection 2013.
CNVannotator: a comprehensive annotation server for copy number variation in the human genome.
Zhao M1, Zhao Z.
:: DESCRIPTION
CNVAnalyst is a Java GUI for statistical, bioinformatic, and visual analyses of CNVs(copy number variants). CNVAnalyst assists in the choice of the optimal CNV calling method and its parameters for each CNV dataset.
::DEVELOPER
Duke Molecular Physiology Institute
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
cvnCapSeq is a set of Java-based command-line tools for detecting and genotyping copy number variation (CNV) in targeted resequencing experiments of large contiguous genomic regions.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
cnvCapSeq: detecting copy number variation in long-range targeted resequencing data.
Bellos E, Kumar V, Lin C, Maggi J, Phua ZY, Cheng CY, Cheung CM, Hibberd ML, Wong TY, Coin LJ, Davila S.
Nucleic Acids Res. 2014 Nov 10;42(20):e158. doi: 10.1093/nar/gku849.
:: DESCRIPTION
cnvHiTSeq is a software for detecting and genotyping CNVs in WGS data
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Genome Biol. 2012 Dec 22;13(12):R120. doi: 10.1186/gb-2012-13-12-r120.
cnvHiTSeq: integrative models for high-resolution copy number variation detection and genotyping using population sequencing data.
Bellos E, Johnson MR, M Coin LJ.
:: DESCRIPTION
SubPatCNV (Subspace Pattern-ming of Copy Number Variations) is a tool for mining CNV subspace patterns, which is able to identify all aberrant CNV regions specific to arbitrary patient subsets larger than a support threshold. SubPatCNV is an approximate association pattern mining algorithm under a spatial constraint on the positional CNV probe features. In the experiments on a large-scale bladder cancer dataset, SubPatCNV discovered many large aberrant CNV events in patient subgroups and also reported CNV regions highly specific to clinical variables such as tumor grade or stage and enriched with more known oncogenes compared with other existing CNV discovery methods.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2015 Jan 16;16(1):16. [Epub ahead of print]
SubPatCNV: approximate subspace pattern mining for mapping copy-number variations.
Johnson N, Zhang H, Fang G, Kumar V, Kuang R.
