liftoveR pipeline

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 citations

 (17)
2018
PMCID: 5797088

[…] 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 […]

2017
PMCID: 5510834

[…] snvs we found that 2,060 (90.75%) and 2,096 (91.73%) gaers and nec-specific snvs successfully mapped from the rat (nov. 2004 [baylor 3.4/rn4]) to the human (feb. 2009 [grch37/hg19]) genome using liftover [33]., of the 307 and 394 gaers- and nec-specific protein-coding indels variant calls, 110 and 154 passed the stringent quality control criteria as previously described for the snv calls. […]

2017
PMCID: 5522221

[…] ucsc database (detail in figure 1, supplementary file table s2 and supplementary file table s3). because the dnase-i hypersensitivity data for the three cell lines are in hg18 coordinate, the ucsc liftover tool [55] is used to convert the hg18 data into hg19. for visualization, the raw data is converted to bed format by using bedtools software [56]., the expression data of the h1-hesc, gm12878 […]

2017
PMCID: 5487215

[…] data were aligned against human genome assembly hg38, some of the datasets were only available on genome assembly hg19 and the coordinates of these datasets were lifted from hg19 to hg38 using liftover (kent et al., 2002) (default re-mapping ratio 0.95). nucleosome positions based on mnase-seq data in gm12878 were determined with danpos version 2.2.2 (chen et al., 2013) using default […]

2017
PMCID: 5703645

[…] 2015; fritsch et al., 2012; stern-ginossar et al., 2012; gao et al., 2015). sites were mapped to hg38 using a chain file from the ucsc genome browser (http://hgdownload.soe.ucsc.edu/goldenpath/hg19/liftover/hg19tohg38.over.chain.gz) and crossmap v0.1.6 (rrid:scr_001173). similar to the methods used in these studies, an altorf is considered as having an active tis if it is associated […]

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