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RDXplorer specifications

Information


Unique identifier OMICS_00349
Name RDXplorer
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format BAM
Operating system Unix/Linux, Mac OS
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes

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No version available

Publication for RDXplorer

RDXplorer citations

 (3)
library_books

Copy number alterations detected by whole exome and whole genome sequencing of esophageal adenocarcinoma

2015
Hum Genomics
PMCID: 4570720
PMID: 26374103
DOI: 10.1186/s40246-015-0044-0

[…] count ratios between a tumor sample and its matched normal sample. these methods can be further categorized according to the study design. some commonly used ones are as follows. (a) cnvnator [], rdxplorer [], and readdepth [] detect cnas on a single tumor sample. (b) cnaseg [], segseq [], exomecnv [], hmmcopy [], and varscan2 [] identify cnas on matched tumor-normal samples. control-freec [, […]

library_books

An integrative framework for the identification of double minute chromosomes using next generation sequencing data

2015
BMC Genet
PMCID: 4423570
PMID: 25953282
DOI: 10.1186/1471-2156-16-S2-S1

[…] of simulated double minute chromosomes. our approach uncovered double minutes with high accuracy, demonstrating its plausibility., although we only tested the framework with three programs (rdxplorer, breakdancer, delly), it can be extended to incorporate results from programs that 1) detect amplified copy number and from programs that 2) detect genomic structural variants like […]

library_books

A survey of tools for variant analysis of next generation genome sequencing data

2013
Brief Bioinform
PMCID: 3956068
PMID: 23341494
DOI: 10.1093/bib/bbs086

[…] in the resulting vcf file, which should hold the phred-log ratio between the likelihood by treating the two samples independently, and the likelihood by requiring the genotype to be identical. cfor rdxplorer the filtered result data set was used. dclever and breakpointer created result files with >2.6 million lines, which need to be further processed. einstallation was aborted due […]


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RDXplorer institution(s)
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA

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