rtracklayer protocols

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rtracklayer specifications

Information


Unique identifier OMICS_09883
Name rtracklayer
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Medium
Version 1.40.6
Stability Stable
Requirements
limma, methods, zlibbioc, tools, BSgenome.Hsapiens.UCSC.hg19, RUnit, GenomicFeatures, R(>=3.3), S4Vectors(>=0.17.25), genefilter, org.Hs.eg.db, humanStemCell, Biostrings(>=2.47.6), GenomicRanges(>=1.31.8), TxDb.Hsapiens.UCSC.hg19.knownGene, GenomeInfoDb(>=1.15.2), Rsamtools(>=1.31.2), IRanges(>=2.13.13), XVector(>=0.19.7), BiocGenerics(>=0.25.1), hgu133plus2.db, GenomicAlignments(>=1.15.6), XML(>=1.98-0), RCurl(>=1.4-2), BSgenome(>=1.33.4), microRNA(>=1.1.1)
Maintained Yes

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Maintainer


  • person_outline Michael Lawrence <>

Publication for rtracklayer

rtracklayer in pipelines

 (16)
2018
PMCID: 5850119
PMID: 29568492
DOI: 10.5256/f1000research.14748.r30355

[…] "ensembl" , seqlevelsstyle(gtex_blood) <- "ucsc" , from the publication , we know the genomic coordinates are mapped to genome reference grch37, so we will have to uplift them to grch38 using rtracklayer and a mapping ("chain") file. the r.utils package is only required to extract the gzipped file:, library(rtracklayer) library(r.utils) # uncomment the following line to download file […]

2018
PMCID: 5850119
PMID: 29568492
DOI: 10.5256/f1000research.14748.r30355

[…] packages #bioclite(c("clusterprofiler", "deseq2", "genomicfeatures", "genomicinteractions", "genomicranges", "ggplot2", "gviz", "gwascat", "interactionset", "recount", "pheatmap", "rcolorbrewer", "rtracklayer", "r.utils", "splitstackshape", "variantannotation")) , we start with a common scenario: we ran a rna-seq experiment comparing patients with a disease and healthy individuals, and would […]

2017
PMCID: 4916993
PMID: 27347385
DOI: 10.5256/f1000research.9514.r14245

[…] ## [30] htmltools_0.3.5 ## [31] tools_3.3.1 ## [32] gtable_0.2.0 ## [33] dorng_1.6 ## [34] rcpp_0.12.9 ## [35] multtest_2.30.0 ## [36] preprocesscore_1.36.0 ## [37] nlme_3.1-131 ## [38] rtracklayer_1.34.2 ## [39] mime_0.5 ## [40] ensembldb_1.6.2 ## [41] rngtools_1.2.4 ## [42] gtools_3.5.0 ## [43] statmod_1.4.29 ## [44] xml_3.98-1.5 ## [45] beanplot_1.2 ## [46] […]

2017
PMCID: 5325622
PMID: 28112643
DOI: 10.7554/eLife.21883.061

[…] (); gviz for plots of chromosome ideograms (); upsetr for plotting overlaps between sets of atac-seq peaks (); genomicranges for calculations involving peak and tss positions in the genome (); rtracklayer () for access to refseq data from the ucsc genome browser database; genomicalignments for manipulating data from paired-end bam files (); deseq2 for calculations of differential gene […]

2016
PMCID: 4794243
PMID: 26982580
DOI: 10.1371/journal.pgen.1005930

[…] pairs with a mapping score > = 30 using samtools []. mononucleosomes were identified as paired-end reads with insert sizes between 50 bp and 240 bp using r bioconductor packages genomicranges, rtracklayer, rsamtools, nucler, and the ucsc saccer3 reference genome [, –]. chip reads were compared to the input reads for each strain using the dynamic analysis of nucleosome and protein occupancy […]


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rtracklayer in publications

 (47)
PMCID: 5928244
PMID: 29712909
DOI: 10.1038/s41467-018-04112-z

[…] all the genes that have tmds expressing ipa isoforms as background., the information about protein domains was obtained from the ucsc uniprot annotation table (spannot) via the bioconductor package-rtracklayer. only the domains with annotation type ‘active site’, ‘domain’, ‘transmembrane region’, ‘repeat’, ‘zinc finger region’, ‘compositionally biased region’, ‘dna-binding region’, ‘region […]

PMCID: 5882905
PMID: 29615825
DOI: 10.1038/s41598-018-24005-x

[…] from a study using the mouse encode data; enhancer prediction was based on chip-seq data of multiple tissues and cell types. data originally mapped to mm9 was lifted over to mm10 using the r package rtracklayer. permutation tests were used to demonstrate the significance of dmcs enrichment. for permutation tests, we randomly sampled n loci of interest (for example, number of dmcs), and count […]

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

[…] packages #bioclite(c("clusterprofiler", "deseq2", "genomicfeatures", "genomicinteractions", "genomicranges", "ggplot2", "gviz", "gwascat", "interactionset", "recount", "pheatmap", "rcolorbrewer", "rtracklayer", "r.utils", "splitstackshape", "variantannotation")) , we start with a common scenario: we ran a rna-seq experiment comparing patients with a disease and healthy individuals, and would […]

PMCID: 5829737
PMID: 29361190
DOI: 10.1093/nar/gky018

[…] portal (). score vectors for 400 bp windows centered around 1000 randomly selected chip-seq peaks within our dataset were retrieved from the bigwig files using a custom r script based on the rtracklayer package. these were assembled into a matrix, which was then sorted by descending row sum and plotted using a custom plotting function., we quantified the correlation between grammatical […]

PMCID: 5756049
PMID: 29267285
DOI: 10.1371/journal.pgen.1007102

[…] repeatmasker open-4.0, 2013–2015. http://www.repeatmasker.org) repeat annotation was downloaded from ucsc (https://genome.ucsc.edu). cpg islands were retrieved from ucsc (“cpgislandext” table) using rtracklayer []. unmethylated (umrs) and low-methylated regions (lmrs) were determined using methylseekr [] on esc and np whole-genome bisulfite data [] with parameters m = 50% and n = 3 (smallest n […]


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rtracklayer institution(s)
Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Channing Laboratory, Harvard Medical School, Boston, MA, USA
rtracklayer funding source(s)
NHGRI (grant P41HG004059 to R.G., in part)

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