gespeR statistics

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Citations per year

Number of citations per year for the bioinformatics software tool gespeR

Tool usage distribution map

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


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




No version available


  • person_outline Niko Beerenwinkel

Publication for Gene-Specific Phenotype EstimatoR

gespeR citations


Measuring inferential importance of taxa using taxon influence indices

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 […]


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

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, 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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