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Literature DB >> 23620362

RSVSim: an R/Bioconductor package for the simulation of structural variations.

Abstract

UNLABELLED: RSVSim is a tool for the simulation of deletions, insertions, inversions, tandem duplications and translocations of various sizes in any genome available as FASTA-file or data package in R. The structural variations can be generated randomly, based on user-supplied genomic coordinates or associated to various kinds of repeats. The package further comprises functions to estimate the distribution of structural variation sizes from real datasets. AVAILABILITY: RSVSim is implemented in R and available at http://www.bioconductor.org. A vignette with detailed descriptions of the functions and examples is included.

Entities: Chemical

Mesh：

Year: 2013 PMID： 23620362 DOI： 10.1093/bioinformatics/btt198

Source DB: PubMed Journal: Bioinformatics ISSN： 1367-4803 Impact factor: 6.937

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Cited

35 in total

1. Joint detection of copy number variations in parent-offspring trios.

Authors: Yongzhuang Liu; Jian Liu; Jianguo Lu; Jiajie Peng; Liran Juan; Xiaolin Zhu; Bingshan Li; Yadong Wang
Journal: Bioinformatics Date: 2015-12-07 Impact factor: 6.937

2. Konnector v2.0: pseudo-long reads from paired-end sequencing data.

Authors: Benjamin P Vandervalk; Chen Yang; Zhuyi Xue; Karthika Raghavan; Justin Chu; Hamid Mohamadi; Shaun D Jackman; Readman Chiu; René L Warren; Inanç Birol
Journal: BMC Med Genomics Date: 2015-09-23 Impact factor: 3.063

3. SVEngine: an efficient and versatile simulator of genome structural variations with features of cancer clonal evolution.

Authors: Li Charlie Xia; Dongmei Ai; Hojoon Lee; Noemi Andor; Chao Li; Nancy R Zhang; Hanlee P Ji
Journal: Gigascience Date: 2018-07-01 Impact factor: 6.524

RSVSim: an R/Bioconductor package for the simulation of structural variations.

1. Joint detection of copy number variations in parent-offspring trios.

2. Konnector v2.0: pseudo-long reads from paired-end sequencing data.

3. SVEngine: an efficient and versatile simulator of genome structural variations with features of cancer clonal evolution.

4. BreakSeek: a breakpoint-based algorithm for full spectral range INDEL detection.

5. BSSV: Bayesian based somatic structural variation identification with whole genome DNA-seq data.

6. Local sequence assembly reveals a high-resolution profile of somatic structural variations in 97 cancer genomes.

7. PSSV: a novel pattern-based probabilistic approach for somatic structural variation identification.

8. SECNVs: A Simulator of Copy Number Variants and Whole-Exome Sequences From Reference Genomes.

9. ScanITD: Detecting internal tandem duplication with robust variant allele frequency estimation.

10. A Sparse Model Based Detection of Copy Number Variations From Exome Sequencing Data.