RCircos protocols

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RCircos specifications

Information


Unique identifier OMICS_04661
Name RCircos
Alternative name runcircos
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 1.2.0
Stability Stable
Requirements
R(≥2.10)
Maintained Yes

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Documentation


Maintainer


  • person_outline Hongen Zhang <>

Additional information


A GUI tool to run Circos is available at: https://github.com/narunlifescience/runcircos-gui

Publication for RCircos

RCircos in pipelines

 (2)
2017
PMCID: 5596349
PMID: 28900023
DOI: 10.1128/mBio.01393-17

[…] frequency and read depth plots generated using custom r scripts were visually inspected and used to confirm the estimated somy for each chromosome. circular chromosomal plots were generated using rcircos ()., fst was calculated using vcftools (), which employs the fst estimate from weir and cockerham’s 1984 paper (). the snp file containing allele information for all 268,518 polymorphic […]

2016
PMCID: 4938650
PMID: 27172215
DOI: 10.1534/g3.116.029504

[…] and inversion breakpoints were analyzed using polymerase chain reaction (pcr)-based sanger sequencing with the primers listed in supplemental material, file s1. inversions were displayed using rcircos () and ingap-sv ()., snpeff v4.0e () was used to annotate the identified snps based on the rnor5.0.74 rat assembly. our previously sequenced individual genome of the ahr sibling species, r. […]


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RCircos in publications

 (31)
PMCID: 5921553
PMID: 29703154
DOI: 10.1186/s12864-018-4698-6

[…] expression were calculated using a bivariate analysis in solar eclipse version 7.6.4. bonferonni corrections were used to account for multiple testing in phenotypic and genetic correlations. we used rcircos package and a modified version of the qqman package in r software to make the circos plot and the chromosomic representations. []. finally, we used the ipa system (ingenuity® systems, […]

PMCID: 5789663
PMID: 29378510
DOI: 10.1186/s12864-018-4487-2

[…] and only three genes between ct and rm (all in opposite directions) (fig. , additional file : table s1). we represented the different shared orthologs between replicons in a circular view (rcircos) in fig. . many regulated gene orthologs were shared between bp and ct (51 blue links in fig. ), while few were shared between all (9 orthologs, green links) and between bp-rm (23 red links) […]

PMCID: 5773557
PMID: 29348663
DOI: 10.1038/s41467-017-02113-y

[…] human reference genome version hg19 by bowtie 2. read numbers in given genomic location were counted by bedtools and normalized by the total mapped reads per sample. circos plot were generated with rcircos based on normalized read numbers. the 4c-seq raw data can be accessed from gene expression omnibus with geo accession number gse103649., subcellular fractionation was performed following […]

PMCID: 5763536
PMID: 29344346
DOI: 10.1186/s13578-018-0202-x

[…] percentage of different small rna species were also analyzed with the statistical data of reads. the distribution of small rna across the whole human genome was performed using a r language package rcircos []. the cumulative frequency distribution was performed using graphpad prism 5, and the relative frequency is shown as a fraction. the correlation analysis was also determined using graphpad […]

PMCID: 5643378
PMID: 29038591
DOI: 10.1038/s41598-017-13650-3

[…] of 341 and 410 genes, we used the intersected genes in both assays for analyses (341 genes). gene fusion rates for single-gene fusions and gene pairs were calculated. for visualization, r package “rcircos” was used to plot circus plots using the hg19 genome build. a gene fusion matrix for each sample was constructed and plotted with r package “pheatmap”., clinically, metastasis […]


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RCircos institution(s)
Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA

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