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Sushi.R specifications

Information


Unique identifier OMICS_09832
Name Sushi.R
Alternative name Sushi
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 1.18.0
Stability Stable
Requirements
graphics, grDevices, R(>=2.10), biomaRt, zoo
Maintained Yes

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Maintainer


  • person_outline Douglas H. Phanstiel <>

Publication for Sushi.R

Sushi.R in publications

 (4)
PMCID: 5953555
PMID: 28922346
DOI: 10.1038/nbt.3968

[…] tads were recalculated based on the merged hi-c matrix by using the same scripts with the same parameters provided in the report. visualization of hi-c data in triangle heatmap was plotted by sushi r package., to compare with gene-oriented interactions deduced from grid-seq data, the normalized hi-c contact map was transformed into a gene-chromatin matrix, much similar to grid-seq […]

PMCID: 5346121
PMID: 28078515
DOI: 10.1007/s10577-016-9546-4

[…] windows in the genome. several bioinformatic packages have been developed for this purpose, such as sushi (phanstiel et al. ), juicebox (durand et al. ) and hicdat (schmid et al. ). with the sushi r package, genomic interaction data, including capture hi-c data, can be plotted along chip-seq, rna-seq and annotation tracks. juicebox enhances exploration of a number of previously published […]

PMCID: 5187580
PMID: 28000665
DOI: 10.1038/ncomms13856

[…] . specific cluster coverage plots were calculated using bedtools genomecov, normalizing to total uniquely aligning reads (excluding small nucleolar rna, transfer rna and mirna), and plotted with the sushi r package from bioconductor., to assay genic pirna reads, 23–29 bp aligned reads were separated into 5′utr, coding sequence and 3′utr regions for each gene (flybase annotations) and counted […]

PMCID: 4499136
PMID: 26007656
DOI: 10.1093/nar/gkv508

[…] were compared using manorm (), and peaks common to both cell lines or cell line specific peaks (p value ≤ 0.01) were determined. read density visualization at specific locations were drawn with sushi.r (). k-mean clusterization of peaks and subsequent visualization were performed with seqminer (). integrative analysis of chipseq, rnaseq and chip-chip data was performed using […]


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Sushi.R institution(s)
Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
Sushi.R funding source(s)
This project is funded by NIH grant U54HG006996 and K99HG007356 and a Damon Runyon fellow supported by the Damon Runyon Cancer Research Foundation (DRG-2122-12).

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