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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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Versioning


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Maintainer


  • person_outline Brett McKinney

Publications for SNPrank

SNPrank citations

 (19)
call_split

WISExome: a within sample comparison approach to detect copy number variations in whole exome sequencing data

2017
Eur J Hum Genet
PMCID: 5865163
PMID: 29255179
DOI: 10.1038/s41431-017-0005-2
call_split See protocol

[…] ara, CA, USA) according to the manufacturer’s protocols. This array consists of over 2.6 million copy number markers. Analysis was done using Nexus software (BioDiscovery, El Segundo, CA, USA), using SNPRank segmentation with a minimum of 20 probes per segment and the significance threshold set at 1e-5. […]

library_books

Integrative information theoretic network analysis for genome wide association study of aspirin exacerbated respiratory disease in South Korean population

2017
BMC Med Genomics
PMCID: 5461529
PMID: 28589859
DOI: 10.1186/s12920-017-0266-1

[…] s 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. propose […]

library_books

PIK3CA mutations are common in lobular carcinoma in situ, but are not a biomarker of progression

2017
PMCID: 5240238
PMID: 28095868
DOI: 10.1186/s13058-016-0789-y

[…] ng 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 ( […]

call_split

The Integration of Epistasis Network and Functional Interactions in a GWAS Implicates RXR Pathway Genes in the Immune Response to Smallpox Vaccine

2016
PLoS One
PMCID: 4981436
PMID: 27513748
DOI: 10.1371/journal.pone.0158016
call_split See protocol

[…] Using the reGAIN matrix from Step 2, we employed an eigenvector centrality algorithm called SNPrank [] to prioritize the variants whose aggregate interactions and main effects contributed most to the variance in the antibody titer. This additional interaction and main-effect filtering step r […]

library_books

Mutation Processes in 293 Based Clones Overexpressing the DNA Cytosine Deaminase APOBEC3B

2016
PLoS One
PMCID: 4862684
PMID: 27163364
DOI: 10.1371/journal.pone.0155391

[…] tion.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 []. All ana […]

library_books

Recurrent Rare Genomic Copy Number Variants and Bicuspid Aortic Valve Are Enriched in Early Onset Thoracic Aortic Aneurysms and Dissections

2016
PLoS One
PMCID: 4836726
PMID: 27092555
DOI: 10.1371/journal.pone.0153543

[…] ed. 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 […]

Citations

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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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