gespeR statistics

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Citations per year

Number of citations per year for the bioinformatics software tool gespeR
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Tool usage distribution map

This map represents all the scientific publications referring to gespeR per scientific context
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Protocols

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 citations

 (2)
call_split

Measuring inferential importance of taxa using taxon influence indices

2018
Ecol Evol
PMCID: 5938459
PMID: 29760889
DOI: 10.1002/ece3.3941
call_split See protocol

[…] ere conducted 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 for thi […]

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Seed effect modeling improves the consistency of genome wide loss of function screens and identifies synthetic lethal vulnerabilities in cancer cells

2017
Genome Med
PMCID: 5452371
PMID: 28569207
DOI: 10.1186/s13073-017-0440-2

[…] take into account the seed-mediated off-target effects, were not able to fully extract the reproducible signal from the shRNA data, thereby leading to suboptimal consistency. We also tried the recent gespeR method [] that models the shRNA–target gene relationships based on the seed sequence complementarity to the 3′ UTR of transcripts to estimate geneESs. After tailoring its parameters for these d […]


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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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