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

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Publication for sPARTA package

sPARTA package in publications

 (3)
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 […]

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, […]

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

Anonymous user #1138

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Easy to use and fast.