SeqSIMLA statistics

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Citations per year

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

SeqSIMLA specifications

Information


Unique identifier OMICS_08584
Name SeqSIMLA
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.5
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


Publications for SeqSIMLA

SeqSIMLA citations

 (5)
library_books

cophesim: a comprehensive phenotype simulator for testing novel association methods

2017
F1000Res
PMCID: 5605948
PMID: 28979766
DOI: 10.5256/f1000research.12938.r24718

[…] ion is to use artificial data simulated with specific assumptions.The best existing phenotype simulators, such as: GENOME , Plink , phenosim , CoaSim , Fregene , ForSim , QuantiNemo , GCTA , HapGen , SeqSimla , and SimRare offer qualitative and dichotomous simulated phenotype. But the known phenotype simulation software tools have some limitations, which may prevent customers from using them: (i) […]

library_books

A combined association test for rare variants using family and case control data

2016
BMC Proc
PMCID: 5133518
PMID: 27980639
DOI: 10.1186/s12919-016-0033-x

[…] sequence data for the CEU (Utah residents with Northern and Western European ancestry) and MXL (Mexican ancestry in Los Angeles, California) populations, where each set consists of 10,000 haplotypes. SeqSIMLA [] was used to simulate families and case–control data based on the haplotypes. A total of 50 nuclear families with 3 siblings, where at least one sibling was affected, and 300 cases and 1000 […]

call_split

Effect of Common Genetic Variants of Growth Arrest Specific 6 Gene on Insulin Resistance, Obesity and Type 2 Diabetes in an Asian Population

2015
PLoS One
PMCID: 4540485
PMID: 26284522
DOI: 10.1371/journal.pone.0135681
call_split See protocol

[…] risons. We generated a population of haplotypes of the four SNPs based on the haplotype frequencies. Consequently, the simulated data had a LD structure similar to real data. The simulation software, SeqSIMLA [], was then used to simulate 1,000 replicates of families with the same family structures to the real data based on the haplotypes. The real trait values were kept in the simulations so that […]

library_books

Adaptive Combination of P Values for Family Based Association Testing with Sequence Data

2014
PLoS One
PMCID: 4277421
PMID: 25541952
DOI: 10.1371/journal.pone.0115971

[…] We generated sequence data with the SeqSIMLA software , which was designed to simulate sequence data for family samples. SeqSIMLA used GENOME as the default sequence generator that could efficiently simulate sequence data according to […]

call_split

Family Based Association Test Using Both Common and Rare Variants and Accounting for Directions of Effects for Sequencing Data

2014
PLoS One
PMCID: 4171487
PMID: 25244564
DOI: 10.1371/journal.pone.0107800
call_split See protocol

[…] erent sizes of regions, 10 kb and 25 kb, were simulated for each simulation replicate. The 10 kb and 25 kb regions had an average of 198 and 512 variants, respectively.We used the simulation software SeqSIMLA to generate family data and disease status based on the sequences generated by cosi. The prevalence model in SeqSIMLA, which is based on a logistic penetrance function with odds ratios and p […]


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SeqSIMLA institution(s)
Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli, Taiwan

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