annotatr statistics

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Citations per year

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Popular tool citations

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annotatr specifications

Information


Unique identifier OMICS_11192
Name annotatr
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.6.0
Stability Stable
Requirements
AnnotationDbi, methods, stats, IRanges, GenomicRanges, utils, testthat, rtracklayer, BiocStyle, dplyr, ggplot2, GenomicFeatures, rmarkdown, knitr, reshape2, org.Hs.eg.db, org.Mm.eg.db, regioneR, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, AnnotationHub, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Mmusculus.UCSC.mm10.knownGene, readr, R(>=3.4.0), devtools, TxDb.Mmusculus.UCSC.mm9.knownGene, roxygen2, GenomeInfoDb(>=1.10.3), S4Vectors(>=0.17.5), org.Dm.eg.db, org.Gg.eg.db, org.Rn.eg.db, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Ggallus.UCSC.galGal5.refGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Rnorvegicus.UCSC.rn5.refGene, TxDb.Rnorvegicus.UCSC.rn6.refGene
Maintained Yes

Taxon


  • Invertebrates
    • Drosophila melanogaster
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus

Download


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Versioning


No version available

Documentation


Maintainers


  • person_outline Raymond Cavalcante
  • person_outline Maureen Sartor

Publication for annotatr

annotatr citations

 (2)
library_books

Usability of human Infinium MethylationEPIC BeadChip for mouse DNA methylation studies

2017
BMC Bioinformatics
PMCID: 5688710
PMID: 29141580
DOI: 10.1186/s12859-017-1870-y

[…] priority was given: ts200 > tss1500 > 5’utr > 1st exon > body >3’utr > igr. overlap of mepic probes with cpg islands, shores, shelves or open sea was determined using the “annotatr” (version v1.1.3) bioconductor package []. fantom5 enhancers were downloaded from http://fantom.gsc.riken.jp/5/datafiles/latest/extra/enhancers/ and overlap with mepic probes was determined […]

library_books

Detection of differential DNA methylation in repetitive DNA of mice and humans perinatally exposed to bisphenol A

2016
Epigenetics
PMCID: 4939917
PMID: 27267941
DOI: 10.1080/15592294.2016.1183856

[…] loci identified as significantly differentially methylated by edger were analyzed for their distribution throughout the hg19 and mm10 genomes for each species. the r software package ‘annotatr’ was used to match by overlap and summarize the individual transposon insertions by chromosomal location with the genomic features listed in (https://github.com/rcavalcante/annotatr). […]


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annotatr institution(s)
Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA; Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
annotatr funding source(s)
Supported by a Bioinformatics Training Grant (National Institute of General Medical Sciences-T32 GM070499) and by National Cancer Institute grant R01 CA158286 and National Institute of Environmental Health Sciences grant P30 ES017885.

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