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OmicCircos specifications

Information


Unique identifier OMICS_04659
Name OmicCircos
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Medium
Version 1.19.0
Stability Beta
Requirements
methods, GenomicRanges, R(>=2.14.0)
Maintained Yes

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Publication for OmicCircos

OmicCircos citations

 (15)
library_books

Integrative genomic and transcriptomic analysis of leiomyosarcoma

2018
Nat Commun
PMCID: 5762758
PMID: 29321523
DOI: 10.1038/s41467-017-02602-0

[…] RNA read. Fusion transcripts were determined using the TopHat2 post-alignment pipeline, and candidates with a score >300 were selected for further analysis. Circos plots were drawn with the R package OmicCircos. […]

library_books

High Density Single Nucleotide Polymorphism (SNP) Mapping and Quantitative Trait Loci (QTL) Analysis in a Biparental Spring Triticale Population Localized Major and Minor Effect Fusarium Head Blight Resistance and Associated Traits QTL

2018
Genes
PMCID: 5793172
PMID: 29304028
DOI: 10.3390/genes9010019

[…] p diagrams illustrating QTL positions were drawn using MapChart software (version 2.32) []. A Circos diagram representing the epistatic interactions in a circular network plot was generated using the OmicCircos (version 1.14.0) package [] in R version 3.2.3 []. […]

library_books

Comparative genomic analysis of a new tellurite resistant Psychrobacter strain isolated from the Antarctic Peninsula

2018
PeerJ
PMCID: 5822837
PMID: 29479501
DOI: 10.7717/peerj.4402

[…] 20 GenBank formatted file (NZ_LIQB00000000.1) using the plotMyGBK wrapper script (https://github.com/microgenomics/plotMyGBK); plotMyGBK uses BioPython and the R platform with the packages rSamTools, OmicCircos, and data.table to produce a vector image of a circular map (; ; ; ; https://github.com/Rdatatable/data.table). […]

library_books

Are Fusion Transcripts in Relapsed/Metastatic Head and Neck Cancer Patients Predictive of Response to Anti EGFR Therapies?

2017
PMCID: 5702394
PMID: 29259349
DOI: 10.1155/2017/6870614

[…] eparated by 100.000 bp distance; (ii) spanning reads on both sides should have at least 13 bp; and (iii) reads map to multiple locations (>2). The annotated gene fusions were then displayed using the OmicCircos software package [] with respect to genomic position using the hg19 reference. […]

call_split

Guanylate binding protein 1 is a potential new therapeutic target for triple negative breast cancer

2017
BMC Cancer
PMCID: 5688804
PMID: 29115931
DOI: 10.1186/s12885-017-3726-2
call_split See protocol

[…] ands (HMM CG Islands) [] were performed with FDb.InfiniumMethylation.hg19 []. Shore, shelf and open sea extension of CG Islands was determined with GenomicRanges []. Circos plot [] was performed with OmicCircos []. […]

call_split

TDP2 suppresses chromosomal translocations induced by DNA topoisomerase II during gene transcription

2017
Nat Commun
PMCID: 5550487
PMID: 28794467
DOI: 10.1038/s41467-017-00307-y
call_split See protocol

[…] CCT-3′). Novel-size bands were purified from agarose gel and sequenced using MLLBgl2_4 or MLLSac1_5 (5′-AGTGCAGTGGCGTGATAATG-3′) primers. Translocations were represented as by a Circos plot using the OmicCircos package of R. […]

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OmicCircos institution(s)
Center for Biomedical Informatics and Information Technology, National Cancer Institute, Chinakville, MD, USA

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