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sPARTA package specifications

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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

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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

[…] 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., protein-coding genes were predicted using multiple gene annotation […]

library_books

Efficient occupancy model fitting for extensive citizen science data

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

[…] for model b we always assume a random effect., model c was fitted separately to each year using unmarked in r, as in the application to bnm data. model b was fitted using a subset of r code from the sparta package []; we ran 3 chains and 10,000 iterations, with the first 20% discarded for burn-in and thinned by taking every third iteration. detection probability was assumed to be constant, […]

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

[…] 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 […]


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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.