EIGENSOFT pipeline

EIGENSOFT specifications

Information


Unique identifier OMICS_07868
Name EIGENSOFT
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 6.0.1
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Samuela Pollack <>

Publications for EIGENSOFT

EIGENSOFT IN pipelines

 (40)
2018
PMCID: 5805289
PMID: 29420653
DOI: 10.1371/journal.pone.0192446

[…] of the populations based on the deleteriousness they harbored for cardiovascular diseases was assessed by principal component analysis (pca) using the plink tool (v1.90b3.30) [44] and verified by eigensoft’s smartpca (version 3.0) [45]., annotation of the variants in genes set related to cardiovascular diseases were carried out using the clinvar data release 20160104 [27]. the allele […]

2018
PMCID: 5877975
PMID: 29463742
DOI: 10.1073/pnas.1716839115

[…] taino; palikur, x), where x is the test population, to test whether any other other native american group in our dataset is more closely related to the taino than the palikur (fig. 1b)., we used eigensoft (102) to calculate pairwise fst distances based on allele frequencies in our dataset. the distance matrix was then used to build a neighbor-joining tree using the ape package in r (56). […]

2017
PMCID: 5452641
PMID: 28472322
DOI: 10.1093/gbe/evx089

[…] maximum likelihood) implemented in gcta to estimate narrow sense heritability (vg/vp). to evaluate the influence of population structures on our observed phenotype, we used the smartpca program of eigensoft 5.0.2 (patterson et al. 2006) to identify top principle components (pcs) from the snp data. we then used the projection length of each strain on the first and second pcs to test […]

2017
PMCID: 5483232
PMID: 28552360
DOI: 10.1016/j.cub.2017.05.023

[…] criteria., principal components were defined using a eurasian subset of the modern data and ancient individuals were projected onto the resulting eigenvectors. this analysis was carried out using eigensoft 5.0.1 smartpca [44], removing one snp from each pair in linkage disequilibrium with r2 > 0.2 [4] and without removing outlying data., we used outgroup f3-statistics [97, 98] to evaluate […]

2017
PMCID: 5520280
PMID: 28174340
DOI: 10.1136/thoraxjnl-2016-208448

[…] were excluded as appropriate (40 individuals; see online supplementary material for further details). qc was undertaken using plink v.1.07 (purcell s; http://pngu.mph.harvard.edu/purcell/plink),17 eigensoft (v.4.2)18 19 and r v.2.15 (r core team; http://www.r-project.org)., , imputation was undertaken using the 1000 genomes project reference panel (1000g phase i integrated release v.3 (march […]

EIGENSOFT institution(s)
Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA

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