liftoveR protocols

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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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Maintainer


  • person_outline Eyal Ben David <>

liftoveR in pipelines

 (123)
2018
PMCID: 5766238
PMID: 29293496
DOI: 10.1371/journal.pcbi.1005921

[…] 450 level 3 data were downloaded from the broad tcga gdac (http://gdac.broadinstitute.org) using firehose_get. the coordinates of the methylation sites (hg18) were converted into hg38 using the ucsc liftover and further intersected with that of the core promoters (hg38). for each gene, we computed the median of the beta values of the methylation sites present in the core promoter […]

2018
PMCID: 5766238
PMID: 29293496
DOI: 10.1371/journal.pcbi.1005921

[…] not detected (no read) in any of the considered samples were removed from the analyses. expression data were log transformed., all sequences were mapped to the hg38 human genome and the ucsc liftover tool was used when necessary. gene tss positions were extracted from gencodev24. utr and cds coordinates were extracted from ensembl biomart. to assign only one 5utr sequence to one gene, […]

2018
PMCID: 5766238
PMID: 29293496
DOI: 10.1371/journal.pcbi.1005921

[…] ucsc table browser or bedtools getfasta []., tcga isoform tsss were retrieved from https://webshare.bioinf.unc.edu/public/mrnaseq_tcga/unc_hg19.bed and converted into hg38 coordinates with ucsc liftover. for other regulatory regions associated to transcript isoforms (utrs, cds, introns and dfr), we used gencode v24 annotations., the nucleotide (n = 4) and dinucleotide (n = 16) percentages […]

2018
PMCID: 5780461
PMID: 29362391
DOI: 10.1038/s41598-018-19782-4

[…] significance level of 0.01., enrichment analysis of chip-seq tf-binding was carried out for each cnv region by (i) mapping to the corresponding region in the human hg19 genome assembly using liftover, (ii) counting the number of chip-seq experiments supporting binding of a tf according to encode’s factorbook, and (iii) assessing statistical significance of the observed evidence […]

2018
PMCID: 5796731
PMID: 29360820
DOI: 10.1371/journal.pgen.1007180

[…] drosophila transcription network project (bdtnp) site [], bed files were downloaded for the hb (anti-hb (antibody 2), stage 9) chip-chip experiment (symmetric-null test and 1% fdr cutoff). the liftover tool from ucsc browser [] was used to transform the dm2 coordinates into the dm3 assembly. the closest gene to each chip-chip interval was identified with the script annotatepeaks.pl […]


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liftoveR in publications

 (771)
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, […]

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 […]

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)., […]

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 […]

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, […]


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