geneXtendeR protocols

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geneXtendeR specifications

Information


Unique identifier OMICS_13292
Name geneXtendeR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A list of peak coordinates data (chromosome, peak start position, peak end position).
Input format TXT
Output data An annotated peaks file consisting of gene IDs, gene names, and proximity information (i.e., distance of peak to nearest gene).
Output format TXT
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, RColorBrewer, graphics, utils, rtracklayer, BiocStyle, dplyr, data.table, rmarkdown, knitr, GO.db, org.Hs.eg.db, org.Mm.eg.db, org.Ce.eg.db, org.Sc.sgd.db, org.Dm.eg.db, org.Gg.eg.db, org.Rn.eg.db, R(>=3.3.1), networkD3, org.Ag.eg.db, org.Bt.eg.db, org.Cf.eg.db, org.Dr.eg.db, org.Mmu.eg.db, org.Pt.eg.db, org.Ss.eg.db, org.Xl.eg.db, SnowballC, tm, wordcloud
Maintained Yes

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Maintainer


  • person_outline Bohdan B. Khomtchouk <>

Publication for geneXtendeR

geneXtendeR in pipeline

2016
PMCID: 5677579
PMID: 27573876
DOI: 10.1038/mp.2016.131

[…] regions. we defined a ‘gene region’ to encompass 3000 bp upstream of the first exon genomic position through 500 bp downstream of the last exon genomic position (http://github.com/bohdan-khomtch-ouk/genextender). to assess the biological variability, edger was used to identify h3k9me1-enriched regions that exhibited significant differences in control as compared with postdependent samples (n = […]


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geneXtendeR in publication

PMCID: 5677579
PMID: 27573876
DOI: 10.1038/mp.2016.131

[…] regions. we defined a ‘gene region’ to encompass 3000 bp upstream of the first exon genomic position through 500 bp downstream of the last exon genomic position (http://github.com/bohdan-khomtch-ouk/genextender). to assess the biological variability, edger was used to identify h3k9me1-enriched regions that exhibited significant differences in control as compared with postdependent samples (n = […]


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geneXtendeR institution(s)
Department of Biology, Stanford University, Stanford, CA, USA; Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL, USA; John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
geneXtendeR funding source(s)
Supported by the Army Research Office (ARO), National Defense Science and Engineering Graduate (NDSEG) Fellowship, 32 CFR 168a.

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