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Sushi.R specifications


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
graphics, grDevices, R(>=2.10), biomaRt, zoo
Maintained Yes




No version available



  • person_outline Douglas H. Phanstiel

Publication for Sushi.R

Sushi.R citations


Chromatin immunoprecipitation (ChIP) method for non model fruit flies (Diptera: Tephritidae) and evidence of histone modifications

PLoS One
PMCID: 5854383
PMID: 29543899
DOI: 10.1371/journal.pone.0194420

[…] ence genome. After performing read alignment and, peak calling was carried out using MACS2 software, and genomic regions displaying enrichment for specific histone proteins were visualised using the ‘Sushi.R’ R/Bioconductor package []. Example peak data for histone proteins H3K4me3, H3K27Ac, H3K36me1 and H3K36me3 are presented in , which evidences histone modification in various genomic regions of […]


Transcriptome Analysis Identifies a 140 kb Region of Chromosome 3B Containing Genes Specific to Fusarium Head Blight Resistance in Wheat

Int J Mol Sci
PMCID: 5877713
PMID: 29538315
DOI: 10.3390/ijms19030852

[…] ples were filtered. Then edgeR [] were used to calculate the RPKM value (RPKM represents reads per kilobase and per million) according to the abundance data for each gene in the 12 samples. R package Sushi [] was used to explore the gene expression distribution on chromosome physical maps. […]


Using regulatory genomics data to interpret the function of disease variants and prioritise genes from expression studies

PMCID: 5850119
PMID: 29568492
DOI: 10.5256/f1000research.14748.r30355

[…] nomic locations to genes. While options for the visualisations of genomic data and interactions are outside the scope of this workflow, at least three good alternatives exist in Bioconductor: ggbio , Sushi and Gviz coupled with the GenomicInteractions package . We refer the reader to these publications and package vignettes for examples.As the sample size and power of GWASs and gene expression s […]


Ensemble genomic analysis in human lung tissue identifies novel genes for chronic obstructive pulmonary disease

Hum Genomics
PMCID: 5769240
PMID: 29335020
DOI: 10.1186/s40246-018-0132-z

[…] The R package Sushi [] was used with gene annotation and regulatory information from Ensemble BioMart [] (CTCF Binding Site, TF binding site, Open chromatin, Promoter and Enhancer information produced from ENCODE, […]


RNA dependent RNA targeting by CRISPR Cas9

PMCID: 5796797
PMID: 29303478
DOI: 10.7554/eLife.32724.036

[…] nificantly enriched guides were defined as those with an FDR-corrected p-value<0.05. Guides with a positive fold-change compared to the control were mapped to the MS2 genome and visualized using the ‘Sushi’ package (). To examine for nucleotide composition bias, sequences of guides with a significant positive enrichment were aligned at the 3´ end (PAM-proximal) and motifs were analyzed using the W […]


Topological organization and dynamic regulation of human tRNA genes during macrophage differentiation

Genome Biol
PMCID: 5607496
PMID: 28931413
DOI: 10.1186/s13059-017-1310-3

[…] generated using the deeptools computeMatrix tool with specified distances from strand-oriented tRNA genes [, ]. Signal track visualization and in situ Hi-C integration plots were generated using the Sushi package for genomic visualization []. Genome-wide tRNA gene circle visualization plots were generated using the RCircos package for Circos 2D track plots []. tDNA interactome network maps were g […]


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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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