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GenomeGraphs specifications

Information


Unique identifier OMICS_10938
Name GenomeGraphs
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.40.0
Stability Stable
Requirements
methods, grid, R(>=2.10), biomaRt
Maintained Yes

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Maintainers


  • person_outline James Bullard <>
  • person_outline Steffen Durinck <>

Publications for GenomeGraphs

GenomeGraphs in pipelines

 (2)
2017
PMCID: 5737695
PMID: 28977517
DOI: 10.1093/nar/gkx778

[…] using bedtools (). clip-seq/rna-seq coverage plots were calculated using coveragebed from the bedtools toolset and visualized using custom scripts in r. gene models were generated using r package genomegraphs ()., alternative poly(a) (apa) site usage was estimated using dapars (). apa events with adjusted p-value < 0.05 were considered significant. for motif analysis, binding sites […]

2012
PMCID: 3324506
PMID: 22509283
DOI: 10.1371/journal.pone.0034238

[…] phage lambda. the output of bwa-sw was converted to binary alignment format (bam) using samtools . coverage plots were generated from the bam files using r, bioconductor and the package genomegraphs . exact global-local nucleotide alignments of all assembled reads against the enterobacteria phage lambda genome (refseq accession nc_001416.1) were computed using the needleman-wunsch […]


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GenomeGraphs in publications

 (13)
PMCID: 5809386
PMID: 29449961
DOI: 10.1038/s41421-017-0006-x

[…] cells were trypsinized with tryple. cdh26a was silenced by transfecting shrna plasmids using the neon transfection system, as detailed in the ., transcript models (top of fig. ) were plotted using genomegraphs r package v3.3. whole transcriptome rna-seq libraries were generated with a modified kapa protocol and sequenced as single end reads on ion torrent proton. isoform expression […]

PMCID: 5737695
PMID: 28977517
DOI: 10.1093/nar/gkx778

[…] using bedtools (). clip-seq/rna-seq coverage plots were calculated using coveragebed from the bedtools toolset and visualized using custom scripts in r. gene models were generated using r package genomegraphs ()., alternative poly(a) (apa) site usage was estimated using dapars (). apa events with adjusted p-value < 0.05 were considered significant. for motif analysis, binding sites […]

PMCID: 5445373
PMID: 28545391
DOI: 10.1186/s12859-017-1687-8

[…] in the sections. next, the model is applied to three case studies in the sections. the paper is concluded with a discussion and conclusion. illustrations are based on the r packages biomart and genomegraphs []. reids is currently bundled in a package publicly available on r-forge., three data sets are used to illustrate the proposed random effects model for the identification of alternative […]

PMCID: 4935837
PMID: 27383233
DOI: 10.1038/srep28998

[…] into gene symbols for testing overlaps with fmrp-binding mrnas or autism-associated mrnas () using the geneoverlap package in bioconductor. probeset and exon plots were produced using the genomegraphs package in bioconductor., the full-length of foxp2 3′ utr was amplified by pcr using the forward primer 5′-tcgcgactagtgaacgaacttgtgacacctcagtg-3′ and reverse primer […]

PMCID: 4818925
PMID: 27042203
DOI: 10.1186/s13029-016-0052-z

[…] is a widely used language and software environment for statistical computing and graphics. several programming tools have been developed under r environment for visualizing genomic data, including genomegraphs [], ggbio [], and gviz []. within these packages, individual types of genomic features or data are represented by separate tracks, and there are constructor functions to coordinate […]


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GenomeGraphs institution(s)
Division of Biostatistics, University of California, Berkeley, Berkeley, CA, USA; Department of Statistics, University of California, Berkeley, Berkeley, CA, USA
GenomeGraphs funding source(s)
Supported by Reshetko Family Endowed Scholarships, NIH Genomics Training Grant, NIH grant U01 HG004271 and NSF Bioinformatics Postdoctoral Fellowship.

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