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Sleipnir specifications

Information


Unique identifier OMICS_19704
Name Sleipnir
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
Computer skills Advanced
Version 3.0
Stability Stable
Requirements
GNU Gengetopt
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Olga G. Troyanskaya

Additional information


https://bitbucket.org/libsleipnir/sleipnir/overview

Publication for Sleipnir

Sleipnir citations

 (18)
library_books

Optimization of moderators and beam extraction at the ESS1

2018
J Appl Crystallogr
PMCID: 5884385
PMID: 29657564
DOI: 10.1107/S1600576718002406

[…] advanced neutron scattering instrumentation, marking the 50th anniversary of the journal., private communications in 2014 and 2015 from m. strobl (odin), m. morgano (odin), a. jackson (loki, skadi, sleipnir), s. jaksch (skadi), h. wacklin (freia), j. stahn (estia), s. mattauch (heritage), d. lott (heritage), a. ioffe (heritage), p. henry (hod), b. rosendahl hansen (hod), c. zendler (dream, […]

library_books

Machine Learning Analysis Identifies Drosophila Grunge/Atrophin as an Important Learning and Memory Gene Required for Memory Retention and Social Learning

2017
PMCID: 5677163
PMID: 28889104
DOI: 10.1534/g3.117.300172

[…] () package. the gene-expression values were then normalized and summarized using the medianpolish method (). the resulting experimental collections were then combined for learning using c++ sleipnir library ()., our gold standard was curated to include known learning and long-term memory genes. our negative standards were selected by pilgrm in a randomized manner. following […]

library_books

A novel multi network approach reveals tissue specific cellular modulators of fibrosis in systemic sclerosis

2017
Genome Med
PMCID: 5363043
PMID: 28330499
DOI: 10.1186/s13073-017-0417-1

[…] file contains the tissue consensus genes from 4ab or the immune–fibrotic axis consensus genes., the giant functional genomic networks were obtained as binary (.dab) files and processed using the sleipnir library for computational functional genomics []. we queried all networks (lung, skin, “all tissue”, macrophage) using the immune–fibrotic axis consensus gene sets (as entrez ids) and pruned […]

library_books

Co expression network analysis of duplicate genes in maize (Zea mays L.) reveals no subgenome bias

2016
BMC Genomics
PMCID: 5097351
PMID: 27814670
DOI: 10.1186/s12864-016-3194-0

[…] cutoffs of z score (1.5, 2.0, 2.5 and 3.0) was used as the threshold for the detection of significant edge (interaction) between genes. the co-expression networks were created and analyzed using the sleipnir c++ library []. the software cytoscape 3.0.2 [] was used for visualization of the co-expression networks. the co-expression network could be explored through the cob database []. due […]

library_books

The Integration of Epistasis Network and Functional Interactions in a GWAS Implicates RXR Pathway Genes in the Immune Response to Smallpox Vaccine

2016
PLoS One
PMCID: 4981436
PMID: 27513748
DOI: 10.1371/journal.pone.0158016

[…] network scale. the filtering steps can be carried out with our command line tools [], and we plan to simplify integration with imp in a future implementation of the command line tool using the sleipnir c++ library []., as association studies uncover new genes linked to complex immune responses, such as antibody response to vaccination, a major challenge is to understand how multiple […]

library_books

Computational Reconstruction of NFκB Pathway Interaction Mechanisms during Prostate Cancer

2016
PLoS Comput Biol
PMCID: 4831844
PMID: 27078000
DOI: 10.1371/journal.pcbi.1004820

[…] please refer to the ., we integrated high-throughput and heterogeneous functional genomic data (see below) using a naïve bayesian approach with regularization [,]. briefly, as implemented in the sleipnir library, the process first performs a maximum likelihood count to reconstruct the joint probability distribution for each dataset between its discretized data values and the gold standard […]


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Sleipnir institution(s)
Lewis-Sigler Institute for Integrative Genomics, Carl Icahn Laboratory, NJ, USA; Department of Computer Science, Princeton University, Princeton, NJ, USA; Molecular Biology, Princeton University, Princeton, NJ, USA
Sleipnir funding source(s)
Supported by NSF CAREER DBI- 0546275, NIH R01 GM071966, NIH T32 HG003284 and NIGMS Center of Excellence P50 GM071508.

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