UCSC LiftOver statistics

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Citations per year

Number of citations per year for the bioinformatics software tool UCSC LiftOver
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Tool usage distribution map

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UCSC LiftOver specifications

Information


Unique identifier OMICS_19501
Name UCSC LiftOver
Alternative name liftOver program
Software type Pipeline/Workflow
Interface Web user interface
Restrictions to use None
Input data A UCSC-generated over.chain file.
Input format BED
Computer skills Basic
Stability Stable
Maintained Yes

Information


Unique identifier OMICS_19501
Name UCSC LiftOver
Alternative name liftOver program
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use License purchase required
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for UCSC LiftOver

UCSC LiftOver citations

 (130)
library_books

Selection on the regulation of sympathetic nervous activity in humans and chimpanzees

2018
PLoS Genet
PMCID: 5908061
PMID: 29672586
DOI: 10.1371/journal.pgen.1007311

[…] s within the window because π = 0 at invariant sites. We also tested 10 chimpanzee [] and 108 macaque [] genomes. Additionally, we used our 337-bp sequences of the 46 chimpanzee samples. Based on the UCSC liftOver tool, we identified chimpanzee (panTro4) and macaque (rheMac3) positions that are orthologous to human (hg19). CLR is calculated by multiplying the probabilities of all polymorphic sites […]

library_books

Systematic characterization of pan‐cancer mutation clusters

2018
Mol Syst Biol
PMCID: 5866917
PMID: 29572294
DOI: 10.15252/msb.20177974

[…] t to map the genomic mutations to the corresponding amino acids. For the genomic mutation coordinates that were not aligned to the Human reference genome assembly build 37 (i.e., GRCh37), we used the UCSC LiftOver service (Kent et al, ) and transferred these to GRCh37. Jointly, the analyzed TCGA and ICGC mutation datasets covered 40 different tumor types which spanned 23 tissues of origin. Sequenc […]

library_books

Somatic Mitochondrial DNA Mutations in Diffuse Large B Cell Lymphoma

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

[…] Nuclear variants were obtained from the supporting information of the published whole genome sequence analysis of the 40 patients. Genomic coordinates were converted from hg18 to hg19 using the UCSC Liftover tool; 3419 of 3424 variants were successfully converted. The compiled list of variants consisting of nuclear somatic mutations, mitochondrial somatic mutations and mitochondrial private […]

library_books

Mammalian genomic regulatory regions predicted by utilizing human genomics, transcriptomics, and epigenetics data

2018
GigaScience
PMCID: 5838836
PMID: 29618048
DOI: 10.1093/gigascience/gix136

[…] ria: types of regulatory regions (promoters, enhancers, and TFBS), biochemical assays, computational models for combining data, and data sources (tissues, cell lines, traits). Second, by applying the UCSC liftOver tool [], regions that were aligned at the genome scale (by LastZ pair-wise genome alignment []) were fine-mapped to identify target regions with proportion of sequence identity to the or […]

library_books

Conserved DNA Methylation Signatures in Early Maternal Separation and in Twins Discordant for CO2 Sensitivity

2018
Sci Rep
PMCID: 5797081
PMID: 29396481
DOI: 10.1038/s41598-018-20457-3

[…] dtools suite. 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. […]

library_books

Genome wide association study of self reported food reactions in Japanese identifies shrimp and peach specific loci in the HLA DR/DQ gene region

2018
Sci Rep
PMCID: 5773682
PMID: 29348432
DOI: 10.1038/s41598-017-18241-w

[…] SC Genome Browser web-site,. To examine overlap with transcription factor binding sites (TFBS), we created a .bed file for our variants, moved the genome-build coordinates from hg19 to hg38 using the UCSC liftOver tool, and then annotated them using the ReMap 2018 Annotation Tool. […]


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