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liftoveR specifications

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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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  • person_outline Eyal Ben David

liftoveR citations

 (817)
library_books

Cross ancestry genome wide association analysis of corneal thickness strengthens link between complex and Mendelian eye diseases

2018
Nat Commun
PMCID: 5951816
PMID: 29760442
DOI: 10.1038/s41467-018-03646-6

[…] mendelian inheritance in man (omim) portal on 26th july 2016. we converted the genomic locations of cct-associated variants from hg19 (or grch37) to the grch38 human genome build using the software liftover, and extracted all gene transcription start sites that lie within the 1 mega-base (mb) on either side of a given variant., using the software haploreg (version 4.1) and regulomedb v1.1, […]

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

[…] in mammals are accelerated in primates; and phars, in which regions conserved in primates (but not other mammals) are accelerated in humans. conversion to hg19 assembly was performed using the liftover tool from the ucsc genome browser., nss data was obtained as a list of markers with corresponding nss values from srinivasan et al. []. markers with negative values, indicating positive […]

library_books

Colon Cancer Upregulated Long Non Coding RNA lincDUSP Regulates Cell Cycle Genes and Potentiates Resistance to Apoptosis

2018
Sci Rep
PMCID: 5943353
PMID: 29743621
DOI: 10.1038/s41598-018-25530-5

[…] control were called using macs software (version 1.4.0rc2) and filtered for peaks with greater than 5-fold enrichment over non-targeting control. peak positions were converted to hg19 using the ucsc liftover tool (https://genome.ucsc.edu/cgi-bin/hgliftover). genomic occupancy peaks were associated with genes within 300 kb using the genomic regions enrichment of annotations tool (great)., […]

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

[…] 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 […]

library_books

A Census of Tandemly Repeated Polymorphic Loci in Genic Regions Through the Comparative Integration of Human Genome Assemblies

2018
Front Genet
PMCID: 5941971
PMID: 29770143
DOI: 10.3389/fgene.2018.00155

[…] census and landscape as source and target collection., the initial listing of tr is derived for both catalogs from the reference genome (grch38 for the census, hg19 for the landscape converted via liftover mapping) by applying trf (landscape), or trf with 3 other methods (census). see the supplementary materials—appendix for details on parameter setting and output merge operations. thus, […]

library_books

Complex evolution of the GSTM gene family involves sharing of GSTM1 deletion polymorphism in humans and chimpanzees

2018
BMC Genomics
PMCID: 5918908
PMID: 29695243
DOI: 10.1186/s12864-018-4676-z

[…] polymorphisms shared between humans and chimpanzees, we took deletion polymorphism data of chimpanzees from a previous paper [], then lifted these deletions to the human reference genome (hg19) by liftover. the data for this paper can be found in primate structural variation database (http://www.korbel.embl.de/primate_sv/). of the 2770 chimpanzee polymorphic deletions, we were able […]


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