SIXPAC statistics

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Citations per year

Number of citations per year for the bioinformatics software tool SIXPAC
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Protocols

SIXPAC specifications

Information


Unique identifier OMICS_10108
Name SIXPAC
Alternative name Search for Interactions is Probably Approximately Complete
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 1.0.2
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Snehit Prabhu

Publication for Search for Interactions is Probably Approximately Complete

SIXPAC citations

 (3)
call_split

Discovering Genetic Interactions in Large Scale Association Studies by Stage wise Likelihood Ratio Tests

2015
PLoS Genet
PMCID: 4581725
PMID: 26402789
DOI: 10.1371/journal.pgen.1005502
call_split See protocol

[…] he screening: χ 2 ≥ 3 (corresponding to p ≤ 0.39) and p ≤ 10−4, respectively. Thirdly, we test two methods based on the LD-contrast test with different filtering strategies: LD-contrast—no screening. Sixpac—the method of [], which recodes variant genotypes into two binary variables (according to dominant and recessive coding) and then combines LD cases screening with a LD-contrast main test. The s […]

call_split

Chi8: a GPU program for detecting significant interacting SNPs with the Chi square 8 df test

2015
BMC Res Notes
PMCID: 4568583
PMID: 26369336
DOI: 10.1186/s13104-015-1392-5
call_split See protocol

[…] NP interactions in type 1 diabetes were also used for prediction and did not yield a higher accuracy [].We also notice that our method is a more stringent test than the LD-contrast implemented in the SIXPAC [] program. For example SIXPAC reports the SNPs rs10925490 and rs2041140 as significant in the WTCCC bipolar disorder dataset with a p-value of 4.61×10-14. On the other hand the Chi-square 8-df […]

call_split

Analysis pipeline for the epistasis search – statistical versus biological filtering

2014
Front Genet
PMCID: 4012196
PMID: 24817878
DOI: 10.3389/fgene.2014.00106
call_split See protocol

[…] ics. Some interaction studies use optimal searching and computational technology to search the whole space for potential interactions. An ultrafast genome-wide scan approach for SNP–SNP interactions, SIXPAC, employs a randomization searching algorithm – probability approximate complete (PAC) testing – to drastically trim the universe of SNP combinations. The approach samples small groups of cases […]


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SIXPAC institution(s)
Department of Computer Science, Columbia University, New York, NY, USA
SIXPAC funding source(s)
The Microsoft Research PhD Fellowship award; NSF awards 0829882 and 0845677; NIH grant U54 CA121852-06

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