GenomicFeatures protocols

GenomicFeatures specifications

Information


Unique identifier OMICS_19627
Name GenomicFeatures
Alternative name GenomicAlignments
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 1.28.4
Stability Stable
Requirements BiocGenerics, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, AnnotationDbi
Maintained Yes

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Maintainer


  • person_outline Michael Lawrence <>

Publication for GenomicFeatures

GenomicFeatures IN pipelines

 (5)
2016
PMCID: 4870679
PMID: 27189775
DOI: 10.1038/srep26329

[…] reads were aligned with tophat232 to a. niger atcc1015 genome version 4.023 retrieved with gff annotations from http://genome.jgi.doe.gov/aspni7/aspni7.home.html and reads counted with r package “genomicfeatures”33., the yeast codon optimized gluc gene (genscript, usa) was released with ecori and bamhi (both neb) and was ligated into a modified pyx212 plasmid34 containing tpi1 promoter […]

2016
PMCID: 5140770
PMID: 27270437
DOI: 10.1038/onc.2016.167

[…] data was aligned to a reference mouse genome (mm9) using tophat (version 1.3.1) software48. the transcript of mouse genome (mm9) was downloaded from ucsc as implemented in the bioconductor package genomicfeatures. the bioconductor packages rsamtools and deseq were then used to estimate the read count for expression of each gene and to detect differentially expressed (de) genes. for count based […]

2014
PMCID: 3898482
PMID: 24439386
DOI: 10.1016/j.cell.2013.11.043

[…] using tophat (trapnell et al., 2009) with default parameters. the read counts per ensembl gene were computed using the r bioconductor (http://bioconductor.org) packages genomic ranges, rsamtools, genomicfeatures, rtracklayer, leebamviews. count data are in table s6 and are also available from arrayexpress (one per tissue, h2-ab1.hip.gene.counts.txt, h2-ab1.lung.gene.counts.txt) where the rows […]

2014
PMCID: 3898482
PMID: 24439386
DOI: 10.1016/j.cell.2013.11.043

[…] using tophat (trapnell et al., 2009) with default parameters. the read counts per ensembl gene were computed using the r bioconductor (http://bioconductor.org) packages genomic ranges, rsamtools, genomicfeatures, rtracklayer, leebamviews. count data are in table s6 and are also available from arrayexpress (one per tissue, h2-ab1.hip.gene.counts.txt, h2-ab1.lung.gene.counts.txt) where the rows […]

2014
PMCID: 3986071
PMID: 24732968
DOI: 10.1371/journal.pone.0093338

[…] and human respectively) with bowtie allowing for 1 mismatch and unambiguously mapping reads only [18]. reads mapping to annotated ensembl genes were counted to estimate gene expression, using the genomicfeatures r packages. read counts were normalised to library size. transcripts with an average of less than 1 read per group in both comparison groups were excluded from further analysis. […]

GenomicFeatures institution(s)
Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, CA, USA; European Molecular Biology Laboratory Genome Biology Unit, Heidelberg, Germany; The European Bioinformatics Institute, Cambridge, UK; Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
GenomicFeatures funding source(s)
Supported by the National Institutes of Health, National Human Genome Research Group through grants P41 HG004059 and U41 HG004059 and by National Heart, Lung and Blood Institute grants R01 HL086601, R01 HL093076 and R01 HL094635.

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