sPARTA package statistics

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sPARTA package specifications

Information


Unique identifier OMICS_05982
Name sPARTA package
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Publication for sPARTA package

sPARTA package citations

 (3)
library_books

Genome assembly with in vitro proximity ligation data and whole genome triplication in lettuce

2017
Nat Commun
PMCID: 5394340
PMID: 28401891
DOI: 10.1038/ncomms14953

[…] further study; miRNA prediction was performed using the previously reported pipeline. PHAS analyses were conducted as described previously. Genome-wide miRNA target prediction was performed using the sPARTA package with the built-in target-prediction module miRFerno, followed by PARE-based validation of predicted targets. […]

library_books

Efficient occupancy model fitting for extensive citizen science data

2017
PLoS One
PMCID: 5362231
PMID: 28328937
DOI: 10.1371/journal.pone.0174433

[…] , where k is a constant, Gi,t,j is the list length (number of species recorded) at site i in year t on visit j, and at is a random year effect, where at ∼ N(μ, σ). This model forms a component of the Sparta [] package in R []. We assume the following prior distributions: bt ∼ U(−10, 10); σu ∼ U(0, 5); μ ∼ N(0, 10); σ ∼ U(0, 5); k ∼ U(−10, 10).The indicator variable zi is also indexed with respect […]

library_books

MicroRNA Maturation and MicroRNA Target Gene Expression Regulation Are Severely Disrupted in Soybean dicer like1 Double Mutants

2015
PMCID: 4751560
PMID: 26681515
DOI: 10.1534/g3.115.022137

[…] ly expressed miRNA target genes with the current genome annotation, it was necessary to predict and validate individual miRNA target genes. The identification of miRNA targets was performed using the sPARTA package () built-in target prediction module mirFerno. Nine PARE libraries were utilized to validate those targets and targets were determined ‘real’ if the target had an adjusted P-value <0.05 […]

Citations

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sPARTA package institution(s)
Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA; Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA; Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA

sPARTA package reviews

 (3)
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Anonymous user #1139

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Desktop
This was very helpful for whole genome analysis.
Anonymous user #1138's avatar image No country

Anonymous user #1138

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Desktop
Easy to use and fast.