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gitter specifications


Unique identifier OMICS_18030
Name gitter
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data An image.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 1.1.1
Stability Stable
Maintained Yes




No version available


  • person_outline Omar Wagih

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Publication for gitter

gitter citations


Natural variation of chronological aging in the Saccharomyces cerevisiae species reveals diet dependent mechanisms of life span control

PMCID: 5845861
PMID: 29560271
DOI: 10.1038/s41514-018-0022-6

[…] tion at 30 °C, plates were scanned with the EPSON V700 Photo scanner at a resolution of 300 dpi. Size and circularity of the colonies were calculated for six biological replicates using the R package Gitter. Using a similar procedure, trait variation within the “sake × tecc” segregating population was estimated on 12 conditions using 3 biological replicates (Tables ). […]


Bacterial Signaling Nucleotides Inhibit Yeast Cell Growth by Impacting Mitochondrial and Other Specifically Eukaryotic Functions

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

[…] 7, respectively, relative to 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 […]


Genetic interactions and functional analyses of the fission yeast gsk3 and amk2 single and double mutants defective in TORC1 dependent processes

Sci Rep
PMCID: 5345095
PMID: 28281664
DOI: 10.1038/srep44257

[…] X6, h− amk2::natMX6, h− gsk3::hphMX6 amk2::natMX6 and control query h− ade6::natMX6. Colony size was used as a proxy for double/triple mutant fitness. Colony size measurements were obtained using the gitter package in R or the Spotsizer tool. In order to exclude potentially spurious interaction values as a result of linkage, library mutants which fell within 100 kb distance of query mutations were […]


Identifying genes required for respiratory growth of fission yeast

Wellcome Open Res
PMCID: 5133385
PMID: 27918601
DOI: 10.21956/wellcomeopenres.10768.r17607

[…] Quantitation of colony sizes was performed with the gitter R package (v. 1.1.1) ( . For normalisation, we used an in-house tool (Townsend StJ., Rallis C., Bähler J., unpublished data). In brief, absent colonies were […]


Potential Direct Regulators of the Drosophila yellow Gene Identified by Yeast One Hybrid and RNAi Screens

PMCID: 5068961
PMID: 27527791
DOI: 10.1534/g3.116.032607

[…] To determine which TFs showed evidence of binding to yellow enhancer fragments, the images from each 1536-well plate were analyzed using an R package called Gitter ()—an image analysis tool for processing of colony-based screens. Raw plate images used for this analysis are included as File S2. This program detects the grid of colonies on each plate, and t […]


A central role for TOR signalling in a yeast model for juvenile CLN3 disease

PMCID: 5354605
PMID: 28357272
DOI: 10.15698/mic2015.12.241

[…] double mutants were pinned to YES + G418 + Nat in a 1536 format. After three days growth at 30°C, agar plates were imaged using a MultiDoc-It Imaging System (UVP) and processed for analysis using the Gitter image analysis R package . Using Excel, the colony sizes produced by Gitter were normalized to the median colony size of each plate to account for within-plate positional growth effects and dif […]

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gitter institution(s)
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada

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