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liftoveR specifications

Information


Unique identifier OMICS_16566
Name liftoveR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages R
Computer skills Advanced
Version 0.2.1
Stability Stable
Requirements
IRanges, GenomicRanges, Rsamtools, Biostrings, blastn
Maintained Yes

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Documentation


Maintainer


  • person_outline Eyal Ben David

liftoveR citations

 (497)
library_books

Recently evolved human specific methylated regions are enriched in schizophrenia signals

2018
BMC Evol Biol
PMCID: 5946405
PMID: 29747567
DOI: 10.1186/s12862-018-1177-2

[…] ody mass index (BMI) [], and height []. For studies published with hg18 coordinates (BPD, SBP, DBP, HDL, LDL, TG, TC, ADHD, RA), conversion to hg19 was performed using the command line version of the liftOver tool from the UCSC Genome Browser (http://hgdownload.cse.ucsc.edu/downloads.html#utilities_downloads). For BMI and height SNPs, the genomic coordinates were obtained by mapping them to the as […]

library_books

A direct link between MITF, innate immunity, and hair graying

2018
PLoS Biol
PMCID: 5933715
PMID: 29723194
DOI: 10.1371/journal.pbio.2003648

[…] inates of the MITF ChIP-seq peaks found in human primary melanocytes and COLO829 melanoma cells, reported in Webster et al. 2014 [], were converted from genome build GRCh37/hg19 to NCBI37/mm9 (Galaxy Liftover), and putative target genes were identified using GREAT, version 3.0.0 []. For the set of genes that exhibit MITF ChIP-seq peaks within 5 kb of their transcription start site in either direct […]

library_books

Global profiling of protein–DNA and protein–nucleosome binding affinities using quantitative mass spectrometry

2018
Nat Commun
PMCID: 5916898
PMID: 29695722
DOI: 10.1038/s41467-018-04084-0

[…] SWI/SNF, PRC2, and NuRD subunits, with publically available G4-sequencing data (Supplementary Table ). All sequencing datasets were mapped to the human genome build hg38 using the UCSC genome browser liftOver tool. All G4 peaks from the plus and minus strand with overlapping coordinates were combined using bedtools. We used automated permutation-based testing with pybedtools to look for significan […]

library_books

Accurate identification of RNA editing sites from primitive sequence with deep neural networks

2018
Sci Rep
PMCID: 5902551
PMID: 29662087
DOI: 10.1038/s41598-018-24298-y

[…] hila analyses, SNVs were called using SAMtools (Version: 1.3.1) (see “Supplemental materials”). Information on the reference genome, dbSNPs and gene model used in this study are listed in Table . The LiftOver tool was used to convert genomic positions between different species. Homologous RNA editing sites are RNA editing sites of one species that have orthologous sites in another species. The hom […]

call_split

Role of DNA methylation in altered gene expression patterns in adult zebrafish (Danio rerio) exposed to 3, 3’, 4, 4’, 5 pentachlorobiphenyl (PCB 126)

2018
PMCID: 5905506
PMID: 29686887
DOI: 10.1093/eep/dvy005
call_split See protocol

[…] gulatory elements by assigning each gene a regulatory domain. To use GREAT, we converted the genomic coordinates of DMRs from GRCz10 version to Zv9 version of the genome using the UCSC genome browser liftOver utility (https://genome.ucsc.edu/cgi-bin/hgLiftOver). We used default parameters with a basal domain that extends 5 kb upstream and 1 kb downstream of the TSS and conducted gene ontology (GO) […]

library_books

A mega analysis of expression quantitative trait loci (eQTL) provides insight into the regulatory architecture of gene expression variation in liver

2018
Sci Rep
PMCID: 5897392
PMID: 29650998
DOI: 10.1038/s41598-018-24219-z

[…] genotype file included hg17 positions of each variant, a unique dbSNP identifier and both alleles of each individual. We initially removed variants without dbSNP identifiers and then used the program liftover from the UCSC Genome Browser (https://genome.ucsc.edu/util.html) to retrieve the hg19 coordinates of each variant. […]

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