gespeR specifications

Information


Unique identifier OMICS_22786
Name gespeR
Alternative name Gene-Specific Phenotype EstimatoR
Software type Framework/Library, Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 0.99.5
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Niko Beerenwinkel <>

Publication for Gene-Specific Phenotype EstimatoR

gespeR in publications

 (2)
PMCID: 5938459
PMID: 29760889
DOI: 10.1002/ece3.3941

[…] using scripts written by the authors (, , , , , , , , ) in the r environment (r core team ) using the ape (paradis, claude, & strimmer, ), phangorn (schliep, ), stringr (wickham, ), and gesper (schmich et al., ) packages. differences in taxon influence‐based rankings between the two tullimonstrum datasets, and differences in rank by proportion of missing data, were calculated […]

PMCID: 5452371
PMID: 28569207
DOI: 10.1186/s13073-017-0440-2

[…] were calculated by averaging over the top two most essential shrnas against an intended target gene []. in cases of only one shrna per target gene, the shes score was considered as the garp score., gesper [] fits a linear regression model of the shrna–gene target relationship on shes values using elastic net regularization. briefly, we obtained the shrna-target relationship matrix […]


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gespeR institution(s)
Department of Biosystems Science and Engineering, ETH, Zurich, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland; Department of Biology, ETH, Zurich, Switzerland; Biozentrum, University of Basel, Basel, Switzerland; Institute for Tropical Health and Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain; Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
gespeR funding source(s)
Supported by SystemsX.ch, the Swiss Initiative in Systems Biology, under IPhD grant 2009/025 and RTD grants 51RT-0_126008 (InfectX) and 51RTP0_151029 (TargetInfectX); the ETH Zurich Postdoctoral Fellowship Program and the Marie Curie Actions for People COFUND program (grant FEL-13 12–1).

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