OmicCircos protocols

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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 in pipelines

 (2)
2018
PMCID: 5822837
PMID: 29479501
DOI: 10.7717/peerj.4402

[…] 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)., raw sequence data from p. glacincola bnf20 are available online […]

2017
PMCID: 5360010
PMID: 28377753
DOI: 10.3389/fmicb.2017.00456

[…] genes were classified according to the clusters of orthologous groups (cog) nomenclature (). finally, cog annotations were used to plot genes, gc content, gc skew, trna and rrna positions, using the omiccircos v 1.8.1. r package ()., bi-directional best hit searches using blast was used to infer homology between reference genes from swiss-prot and the predicted genes from our exiguobacterium […]


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OmicCircos in publications

 (14)
PMCID: 5762758
PMID: 29321523
DOI: 10.1038/s41467-017-02602-0

[…] 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., fusion transcripts were validated using rt-pcr and sanger sequencing. rna was reverse-transcribed using the high-capacity cdna reverse transcription kit (applied biosystems). […]

PMCID: 5793172
PMID: 29304028
DOI: 10.3390/genes9010019

[…] 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 []., both fhb nurseries had good disease development with notably more fhb development at beloeil (). among parents and common checks, […]

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

[…] 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)., raw sequence data from p. glacincola bnf20 are available online […]

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

[…] 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., the information on genes/lncrna was retrieved from https://www.ncbi.nlm.nih.gov/gene […]

PMCID: 5688804
PMID: 29115931
DOI: 10.1186/s12885-017-3726-2

[…] (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 []., the cancer proteomic atlas (tcpa) reverse phase protein array (rppa) data [] replicate-based normalized [] were obtained from the tcpa data portal (http://tcpaportal.org/tcpa/), […]


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

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