liftoveR protocols

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
Stability Stable
Requirements Biostrings, GenomicRanges, IRanges, Rsamtools, QuasR, Rsubread
Maintained Yes

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Maintainer


  • person_outline Eyal Ben David <>

liftoveR IN pipelines

 (54)
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: 5797081
PMID: 29396481
DOI: 10.1038/s41598-018-20457-3

[…] in order to assess the cross-species consistency of methylation clusters, human cluster coordinates (hg19 assembly) were mapped to orthologous mouse coordinates (mm10 assembly) with the ucsc “liftover” tool (“minmatch” = 0.1). estimation of tissue-specific chromatin state feature enrichment was performed as detailed in supplementary methods., the procedure of the 35% co2 -challenge […]

2018
PMCID: 5797088
PMID: 29396444
DOI: 10.1038/s41598-018-20727-0

[…] relevant the network is to the original list of focus genes., the single tissue cis-eqtl data were downloaded from the gtex website (v6p gtex release, gtex_analysis_v6p_eqtl.tar)29 using the ucsc liftover tool. then, eqtl snps were located in lncrnas and mrnas using bedtools93. fisher’s exact tests were performed using r., for data validation by rt-pcr, human oocyte and cc samples […]

2018
PMCID: 5827201
PMID: 29483551
DOI: 10.1038/s41598-018-21844-6

[…] variants were obtained from the supporting information of the published whole genome sequence analysis of the 40 patients37. genomic coordinates were converted from hg18 to hg19 using the ucsc liftover tool43; 3419 of 3424 variants were successfully converted. the compiled list of variants consisting of nuclear somatic mutations, mitochondrial somatic mutations and mitochondrial private […]

2018
PMCID: 5848805
PMID: 29608722
DOI: 10.1093/gbe/evy041

[…] and barcodes removed. in order to compare dhs sites between species, we bowtie-mapped (langmead et al. 2009) reads to appropriate genomes and brought chimpanzee coordinates to human space using liftover (hinrichs et al. 2006). we called peaks with macs (zhang et al. 2008) using a lower p-value threshold of 1e-5 and found an average of ∼150,000 peaks in human samples, and ∼116,000 peaks […]

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