SNPrank protocols

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SNPrank specifications

Information


Unique identifier OMICS_22147
Name SNPrank
Alternative names pysnprank, matsnprank, jsnprank
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java, MATLAB, Python
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Version 0.1.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Brett McKinney <>

Publications for SNPrank

SNPrank in pipeline

2010
PMCID: 2875020
PMID: 20142258
DOI: 10.1093/nar/gkq040

[…] for simulation 1, nsr optimized parameters or parameters with measurable differences from the optimal parameter. methods ranked from first to last using cnvs were as follows: quantisnp and nexus snprank, penncnv (average roc residual = 0.707), penncnv (0.703), cbs (0.675), glad (0.631), nexus rank (0.598) and cnvfinder (0.061) (c; supplementary table s4). the interquartile ranges (iqrs) […]


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SNPrank in publications

 (15)
PMCID: 5461529
PMID: 28589859
DOI: 10.1186/s12920-017-0266-1

[…] an interaction network using information gain with snp prioritization with evaporative cooling []. davis et al. extended the mckinney et al.’s work using a network eigenvector centrality algorithm (snprank), which is analogous to google pagerank algorithm to detect interactions that have the weak effect [], and gain with a generalized linear model (regain) was also proposed []. hu et al. […]

PMCID: 5240238
PMID: 28095868
DOI: 10.1186/s13058-016-0789-y

[…] dna for each sample was used. labelling and hybridization were outsourced to affymetrix (santa clara, ca, usa)., raw array data was preprocessed with nexus 7.5 software (biodiscovery), applying the snprank segmentation algorithm with a minimum of 10 probes per segment. tumour aberration prediction suite (taps) 2.0 [] was used to determine absolute copy number and for categorisation into: gains […]

PMCID: 4981436
PMID: 27513748
DOI: 10.1371/journal.pone.0158016

[…] incorporate main and interaction effects: simulated evaporative cooling (sec) [], regression model-based genetic association interaction networks (regain) [], and an epistasis network centrality (snprank) []. we have applied these filtering methods in the context of pathway analysis by replicating enriched pathways in gwas of bipolar disorder []. another related approach used an l1 pathway […]

PMCID: 4862684
PMID: 27163364
DOI: 10.1371/journal.pone.0155391

[…] chromosomal abnormalities in the genomes of granddaughter clones were identified with nexus copy number 7.5 software (biodiscovery, hawthorne, ca), using the matched mother clone as a reference. snprank segmentation was applied and the segmented copy number data were further processed with the tumor aberrations prediction suite (taps) to obtain allele-specific copy number profiles []. […]

PMCID: 4836726
PMID: 27092555
DOI: 10.1371/journal.pone.0153543

[…] for penncnv analysis, the report file was split into individual sample files before cnvs were called using a custom-generated population frequency of b allele (.pfb) file. for nexus analysis, the snprank algorithm was used with significance threshold of 1x10-8, default gender set to female and systematic correction based on array type. sample-level quality control analysis was performed using […]


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SNPrank institution(s)
Department of Mathematical and Computer Sciences, University of Tulsa, Tulsa, OK, USA
SNPrank funding source(s)
Supported by National Institutes of Health [Grants no. K25 AI-64625; R56 AI-80932].

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