GeneClust statistics

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Associated diseases

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GeneClust specifications

Information


Unique identifier OMICS_04671
Name GeneClust
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Windows
Programming languages C, Java, R
Computer skills Advanced
Version 1.0.2
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Bradley Broom <>
  • person_outline Kim-Anh Do <>

Information


Unique identifier OMICS_04671
Name GeneClust
Interface Web user interface
Restrictions to use None
Programming languages C, Java, Javascript, R
Computer skills Basic
Stability Stable
Maintained Yes

Maintainers


  • person_outline Bradley Broom <>
  • person_outline Kim-Anh Do <>

Publication for GeneClust

library_books

GeneClust.

2003
DOI: 10.1007/0-387-21679-0_15

GeneClust in publications

 (4)
PMCID: 5433983
PMID: 28515867
DOI: 10.1002/ece3.2839

[…] using euclidean distance (the shortest geographical distance) between population pairs, because populations may not have colonized via current waterways after the last glacial maxima. we used the geneclust package (ancelet, ) in r to estimate pairwise f st between populations (weir & cockerham, ). all geographical distances (euclidean and river) were log‐transformed, and all genetic […]

PMCID: 4267876
PMID: 25540699
DOI: 10.1002/ece3.1305

[…] origin has little or no representation in the dataset. these methods have been shown to perform well at detecting individuals that have migrated, with tess generally performing better than geneland, geneclust, and structure (chen et al. )., these assignment methods can perform well at identifying migrant individuals, but they can be outperformed by assignment-based techniques that also infer […]

PMCID: 3777896
PMID: 24069499
DOI: 10.1371/journal.pntd.0002456

[…] size . we also calculated standardized fst (fst of the sample relative to the maximum fst value possible given the dataset) using recodedata v. 0.1 . to calculate pair-wise theta, we used the geneclust package in r , . we automated the process to iteratively (1) create a one-per-family dataset for each patient and (2) calculate all pair-wise fst values between patients. this process […]

PMCID: 2753593
PMID: 19747394
DOI: 10.1186/1755-8794-2-59

[…] to identify clusters of highly correlated genes, we used unsupervised gene shaving []. specifically, we used a high-performance, parallel c implementation of the method that was developed from the geneclust software package []. gene shaving was used independently on both unweighted data and on 127 bootstrap resamples, extracting the first 150 gene clusters in each case. in both cases, the data […]


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GeneClust funding source(s)
Supported by the National Institute of Health via the University of Texas SPORE in Prostate Cancer (CA90270) and the Early Detection Research Network (Grant CA99007).

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