sangerseqR specifications

Information


Unique identifier OMICS_15991
Name sangerseqR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 1.16.0
Stability Stable
Requirements
methods, BiocGenerics, Biostrings, BiocStyle, RUnit, knitr, shiny, R(>=3.0.2)
Maintained Yes

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Maintainer


  • person_outline Jonathon Hill <>

Publication for sangerseqR

sangerseqR in publications

 (3)
PMCID: 5901500
PMID: 29473935
DOI: 10.1590/1678-4685-GMB-2017-0165

[…] hilden, germany) and sanger-sequenced by seqlab (göttingen, germany). relative peak heights of the snp of interest were quantified using r software version 3.2.4 () applying the add-on package sangerseqr version 1.4.0 (). allelic ratios were calculated and log-transformed (see ). for each snp, the log-transformed allelic ratio was corrected in an assay-specific manner (forward or reverse) […]

PMCID: 5755920
PMID: 29267279
DOI: 10.1371/journal.pgen.1007123

[…] (i.e. unmethylated cytosines, which were converted to uracil by bisulfite treatment, then to thymine by pcr) channels, respectively. the signal intensities were extracted in r 3.3.3 [] using the sangerseqr package (version 1.12.0) []. to estimate the editing rate, regions containing the sgrna target sites was pcr-amplified from unconverted dna using primer sets f5-05 through f5-09. editing […]

PMCID: 5886052
PMID: 28972594
DOI: 10.1038/leu.2017.303

[…] since primer design for this exon in a multiplex amplicon setting failed. chromatograms were visually inspected for the presence of mutations in codons 59 to 63 as well as analyzed by the r package sangerseqr in combination with the tools above to call and annotate detected variants., clinical characteristics were compared using fisher’s exact test in r (version 3.2.1). we analyzed cases […]


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sangerseqR institution(s)
Molecular Medicine Program and Department of Neurobiology & Anatomy, University of Utah School of Medicine, Salt Lake City, UT, USA
sangerseqR funding source(s)
This work was supported by a NHLBI Bench-to-Bassinet Consortium grant and a NRSA fellowship.

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