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PSIKO specifications

Information


Unique identifier OMICS_09303
Name PSIKO
Alternative name Population Structure Inference using Kernel-pca and Optimisation
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format .geno format
Operating system Unix/Linux, Mac OS
Programming languages C++
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Andrei-Alin Popescu

Publications for Population Structure Inference using Kernel-pca and Optimisation

PSIKO citations

 (3)
call_split

Validation of an updated Associative Transcriptomics platform for the polyploid crop species Brassica napus by dissection of the genetic architecture of erucic acid and tocopherol isoform variation in seeds

2017
Plant J
PMCID: 5767744
PMID: 29124814
DOI: 10.1111/tpj.13767
call_split See protocol

[…] analysis for SNPs and GEMs was performed using r, as previously described (Harper et al., ; Sollars et al., ), with modifications. In order to deal with the greatly increased sizes of the data sets, psiko (Popescu et al., ) was used for Q‐matrix generation and the gapit r package was used with a mixed linear model (Lipka et al., ) for GWAS analysis. For Manhattan plots of SNP associations, SNP ma […]

library_books

Identification of Candidate Genes for Calcium and Magnesium Accumulation in Brassica napus L. by Association Genetics

2017
Front Plant Sci
PMCID: 5694822
PMID: 29187860
DOI: 10.3389/fpls.2017.01968

[…] ficant expression (mean > 0.4 RPKM) was detected for 53,889 CDS models. Inference of population structure by Q-matrix was obtained by Population Structure Inference using Kernel-PCA and Optimization (PSIKO; ). A heatmap illustrating the relatedness of all genotypes in this study can be found in Supplementary Figure . Transcriptome sequences are deposited within the Sequence Read Archive () under a […]

library_books

Molecular markers for tolerance of European ash (Fraxinus excelsior) to dieback disease identified using Associative Transcriptomics

2016
Sci Rep
PMCID: 4725942
PMID: 26757823
DOI: 10.1038/srep19335

[…] per kilobase per million aligned reads (RPKM), and 470,494 SNPs were detected as described previously. Population structure in the panel was inferred by using the kernel-PCA and optimisation method, PSIKO, which revealed two main population clusters. The two clusters did not correlate with the geographical locations of the mature trees, but more likely reflect the distribution of specific breedin […]

Citations

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PSIKO institution(s)
School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, UK; Centre for Novel Agricultural Products, Department of Biology, University of York, York, UK; Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich, UK

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