Eigen statistics

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Eigen specifications


Unique identifier OMICS_13236
Name Eigen
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 1.1
Stability Stable
Maintained Yes



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  • person_outline Iuliana Ionita-Laza <>

Publication for Eigen

Eigen in publications

PMCID: 5891078
PMID: 29590102
DOI: 10.1371/journal.pgen.1007293

[…] (dhs) data from multiple cell lines (the sum of the counts for each allele across 46 heterozygous cell types) and erythroblasts were used to assess allelic skew in sequenced reads.[, ] eigen-pc, deepsea, and gkm-svm are algorithms that predict the function of non-coding variants and were used as previously described to in silico predict the effect of common variants.[, , , ] […]

PMCID: 5799157
PMID: 29423277
DOI: 10.1038/s41525-018-0044-9

[…] and siphy), nine functional prediction scores (fathmm, lrt, mutationassessor, mutationtaster, polyphen2-hdiv, polyphen2-hvar, provean, sift and vest3), six general prediction scores (cadd, dann, eigen-pc, fathmm-mkl, fitcons-i6 and genocanyon) and three ensemble scores (m-cap, metalr and metasvm)., we analysed 11,722 hpo 'phenotypic abnormality' terms and found that 6627 […]

PMCID: 5823682
PMID: 29224215
DOI: 10.1002/mgg3.347

[…] of genetic variants was evaluated using polyphen (adzhubei et al., ), the combined annotation‐dependent depletion (cadd) framework (kircher et al., ), an unsupervised spectral approach (eigen) (ionita‐laza, mccallum, xu, & buxbaum, ), the consensus deleteriousness score of missense mutations (condel) (gonzalez‐perez & lopez‐bigas, ), the mendelian clinically applicable […]

PMCID: 5704597
PMID: 29179779
DOI: 10.1186/s13059-017-1353-5

[…] concordances could potentially bias the variant interpretation towards a vus classification if all the other available variant data suggests the opposite assertion., for some algorithms such as eigen [], heat [], gerp [], etc., cut-offs defining pathogenic or benign assertion are either not recommended or inferred arbitrarily. we therefore used the actual output scores provided by all 25 […]

PMCID: 5663107
PMID: 29084591
DOI: 10.1186/s13104-017-2851-y

[…] of these valuable resources, multiple computational approaches have already been developed to annotate genetic variants using genome-wide profiling data including gwava [], cadd [], genocanyon [], eigen, eigenpc [], dann [], fitcons [], fathmm [], deltasvm [], dbnsfp [], funseq 2 [] and icages []. a common feature of those methods is that they are disease/trait neutral, which means […]

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Eigen institution(s)
Department of Biostatistics, Columbia University, New York, NY, USA; Department of Psychiatry, Columbia University, New York, NY, USA; Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA

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