SGAtools specifications


Unique identifier OMICS_18029
Name SGAtools
Interface Web user interface
Restrictions to use None
Programming languages Java
Computer skills Basic
Stability Stable
Maintained Yes



  • person_outline Leopold Parts <>

Publication for SGAtools

SGAtools in publications

PMCID: 5864082
PMID: 29529031
DOI: 10.1371/journal.pgen.1007253

[…] a singer rotor hda, the 384 well cell cultures were stamped onto ypd plates and incubated at 30°c for 2 days. plates were then imaged using a bio-rad gel doc xr system and images processed using sgatools []. the average of the normalized colony size values for replicates of each biological were then combined and used for analysis. we assumed normal distribution on the dataset and used […]

PMCID: 5601920
PMID: 28916784
DOI: 10.1038/s41467-017-00632-2

[…] the fitness in hu as the ratio between the colony size in hu and the colony size in absence of drug. raw colony size for each double mutant grown in absence or presence of hu was determined using sgatools ( and further data analysis was perform in r using a customized pipeline. double mutants displaying small colony size in the absence of drug were removed […]

PMCID: 5633387
PMID: 28839115
DOI: 10.1534/g3.117.300104

[…] used in the mata selection and exposed to the different temperature regimes described in the results section., the image analysis, processing, and fitness scoring of the arrays were done using sgatools ( (). gene ontology (go) enrichment analysis was performed using the generic go term finder ( of princeton […]

PMCID: 5551707
PMID: 28615194
DOI: 10.1083/jcb.201611197

[…] selection medium and incubated for 20 h at 30°c. photographs of the plates were taken using a kodak easyshare dx7590 camera. genetic interactors were identified by visual inspection or using sgatools software (). strains with a genetic interaction score below −0.3 were considered synthetic sick. the sga screen was performed twice and only strains reproducibly found in both screens […]

PMCID: 5527313
PMID: 28743817
DOI: 10.1128/mBio.01047-17

[…] the control query using plasmid pah134. colony areas on scanned images were quantified, spatially normalized, row-column normalized, and then filtered using the r package gitter () and the r script sgatools (). plate normalization was not used, as it makes the assumption that changes in colony size are rare events (), which is incorrect for these sga induction screens ( and ). jackknife […]

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SGAtools institution(s)
Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Department of Computer Science and Engineering, University of Minnesota–Twin Cities, Minneapolis, MN, USA
SGAtools funding source(s)
University of Minnesota Doctoral Dissertation Fellowship; National Institutes of Health grants [1R01HG005853-01, 1R01HG005084-01A1, 1R01HG005853-01]; CIHR grant [MOP-102629]; ORF grant [GL2-01-22]; NSERC Doctoral Postgraduate Scholarship; and Canadian Institute for Advanced Research Fellowship.

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