annotatr statistics

You need an account to access this content

info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Peak annotation Methylation annotation chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

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


Versioning


Add your version

Documentation


Maintainers


  • person_outline Raymond Cavalcante <>
  • person_outline Maureen Sartor <>

Publication for annotatr

annotatr in publications

 (2)
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 […]

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). […]

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.

annotatr reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review annotatr