AlphaSimR statistics

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Citations per year

Number of citations per year for the bioinformatics software tool AlphaSimR
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Tool usage distribution map

This map represents all the scientific publications referring to AlphaSimR per scientific context
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Associated diseases

This word cloud represents AlphaSimR usage per disease context
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Protocols

AlphaSimR specifications

Information


Unique identifier OMICS_33140
Name AlphaSimR
Alternative name AlphaSim
Software type Package/Module
Interface Command line interface
Restrictions to use None
Output data A file providing information about the haplotype sequences, SNP and QTN genotypes, and breeding values.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License MIT License
Computer skills Advanced
Version 0.8.2
Stability Stable
Requirements
methods, R6
Maintained Yes

Versioning


No version available

Documentation


Maintainers


  • person_outline John Hickey
  • person_outline Chris Gaynor

Additional information


The web application is avilable at https://alphagenes.shinyapps.io/alphasimrguif2/ and https://alphagenes.shinyapps.io/alphasimrshiny/.

Information


Unique identifier OMICS_33140
Name AlphaSimR
Alternative name AlphaSim
Interface Web user interface
Restrictions to use None
Output data A file providing information about the haplotype sequences, SNP and QTN genotypes, and breeding values.
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainers


  • person_outline John Hickey
  • person_outline Chris Gaynor

Additional information


The web application is avilable at https://alphagenes.shinyapps.io/alphasimrguif2/ and https://alphagenes.shinyapps.io/alphasimrshiny/.

Publication for AlphaSimR

AlphaSimR citations

 (801)
library_books

The cholinergic contribution to the resting state functional network in non demented Parkinson’s disease

2018
Sci Rep
PMCID: 5955917
PMID: 29769626
DOI: 10.1038/s41598-018-26075-3

[…] simulations were performed to adjust for Type I errors (parameters: individual voxel P = 0.02, simulation = 10,000 times iteratively, 6-mm FWHM Gaussian filter width with a whole-brain mask) with the AlphaSim program, which provided an estimate of the overall significant level in the AFNI to determine a probability of the false positive detection from a frequency count of cluster size. This was ac […]

library_books

Assessment of synchronous neural activities revealed by regional homogeneity in individuals with acute eye pain: a resting state functional magnetic resonance imaging study

2018
PMCID: 5916265
PMID: 29719418
DOI: 10.2147/JPR.S156634

[…] ces in ReHo at different frequency bands in these ROIs between the EP groups and the HCs (P<0.01) for multiple comparisons using Gaussian Random Field (GRF) theory (z>2.3, P<0.01, cluster >40 voxels, AlphaSim corrected). The mean ReHo values in the different brain regions between the two groups were analyzed using receiver operating characteristic (ROC) curves. The Pearson’s correlation was used t […]

library_books

Baseline Brain Activity Changes in Patients With Single and Relapsing Optic Neuritis

2018
Front Hum Neurosci
PMCID: 5919956
PMID: 29731712
DOI: 10.3389/fnhum.2018.00144

[…] 05 and cluster size ≥270 mm3 (10 voxels) were considered to show a significant difference between the two groups. A corrected threshold of p < 0.01 was determined by Monte Carlo simulations using the AlphaSim program (Parameters were a FWHM = 4 mm and a mask of the whole brain gray matter tissue). The significantly different brain regions were superimposed on the standard T1-weighted imaging of th […]

library_books

Trait anger modulates neural activity in the fronto parietal attention network

2018
PLoS One
PMCID: 5908080
PMID: 29672547
DOI: 10.1371/journal.pone.0194444

[…] pplied, combined with a minimum cluster-extent of 26 contiguous voxels (702 mm3), to yield a corrected cluster-level false positive rate of p<0.05 as determined by Monte Carlo simulations (similar to AlphaSim) [] (http://www2.bc.edu/~slotnics/scripts.htm). We examined any interaction effects statistically in SPSS using the extracted cluster values from Marsbar (http://marsbar.sourceforge.net/index […]

library_books

The functional and structural characteristics of the emotion network in alexithymia

2018
PMCID: 5905825
PMID: 29695908
DOI: 10.2147/NDT.S154601

[…] series (WM, CSF, and six head motion parameters were covariates), Fisher’s Z-transformation, voxel-by-voxel based comparisons of FC of 21 ROIs between two groups by two-sample t-test using REST, and AlphaSim correction (p<0.001, AlphaSim correction, cluster size >20)., The result was visualized by BrainNet Viewer (https://www.nitrc.org/projects/bnv/). […]

library_books

Left Parietal Functional Connectivity Mediates the Association Between COMT rs4633 and Verbal Intelligence in Healthy Adults

2018
Front Neurosci
PMCID: 5902573
PMID: 29692704
DOI: 10.3389/fnins.2018.00233

[…] permutation test after controlling the same covariates, results were shown in Figure . Then, to validate our results derived from the connection threshold of 0.6, we also repeated the lrFCD analysis (AlphaSim corrected P < 0.05, voxel P < 0.001) using the connection thresholds 0.7 and 0.5 after controlling the same covariates. For the threshold of 0.7, the genotypic effects of COMT rs4633 on lrFCD […]


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AlphaSimR institution(s)
The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK; CIMMYT, Texcoco, Mexico
AlphaSimR funding source(s)
Supported by The Australian Research Council, Aviagen LTD, Genus PLC, Pfizer Inc., The Sheep CRC, CIMMYT, Advanta Semillas, the Seeds of Discovery Project supported by SAGARPA (La Secretaría de Agricultura, Ganadería, Desarrollo Rural, Pesca y Alimentación), Mexico under the MasAgro (Sustainable Modernization of Traditional Agriculture) initiative, the ISPG funding from the BBSRC, and the GplusE project.

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