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VanillaICE specifications

Information


Unique identifier OMICS_02070
Name VanillaICE
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Robert B. Scharpf <>

VanillaICE in publications

 (4)
PMCID: 5279752
PMID: 28135296
DOI: 10.1371/journal.pone.0170815

[…] and wave-adjusted lrrs were computed as described previously[]. estimates for copy number states 0–4 for all autosomes were derived as previously described for the ea participants using the vanillaice hmm[, ]. we required at least 10 markers in a cnp region identified by the hmm to reduce false positive identifications. we excluded 393 ea and 275 aa subjects for one […]

PMCID: 5327642
PMID: 28255359
DOI: 10.7150/thno.16357

[…] raw probe intensity data (cel files) obtained from the genechip scanner 3000 system (affymetrix) were imported to r, segmented using crlmm algorithm and copy number variantion was estimated by the vanillaice and dnacopy methods., after protein extraction, the protein concentration was determined using bca protein quantification kit. the samples (50 μg of protein/lane) were separated on a 12% […]

PMCID: 4118309
PMID: 25007794
DOI: 10.1186/1471-2156-15-81

[…] arraytv [] – an approach adapted from software for removing waves in high-throughput sequencing data []. a 6-state hmm comprising 5 distinct copy number states (0-4) implemented in the r package vanillaice (vi) and the stand-alone tool penncnv were applied independently to each sample [,,]. cnvs with fewer than 10 markers were excluded due to the level of noise of the log r ratios […]

PMCID: 3146450
PMID: 21627824
DOI: 10.1186/1471-2105-12-220

[…] number specific quality-control metrics and identified 136 poor cnv samples. regions of copy number variation (cnv) were detected using the hidden markov models provided within penncnv and crlmm/vanillaice. penncnv detected more cnvs than crlmm/vanillaice; the median number of cnvs detected per sample was 39 and 30, respectively. penncnv detected most of the regions that crlmm/vanillaice […]


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