ParticleStats
Open source software for the analysis of intracellular particle motility and cytoskeletal polarity. ParticleStats was created by Russell Hamilton and Ilan Davis at the Department of Biochemistry, University of Oxford and in collaboration with the Micron Advanced Imaging Facility.
[More Details] [View on GitHub]
Hamilton, R.S., Parton, R.M., Oliveira, R.A., Ball, G., Vendra, G., Nasmyth, K. & Davis, I. (2010) ParticleStats: Open source software for the analysis of intracellular particle motility. Nucl. Acids Res. Web Server Edition [DOI]
TrackAlign
TrackAlign is a suite of tools to allow the comparison and evaluation of tracking algorithms. The aim of the project is to determine the most appropriate tracking algorithm to use for a particular data set and to select the optimal parameters for the tracking.
Project Status: Main code finished :: Statistics under development ::: Paper under preparation
ContactMaps
Open software for the generation of images and analysis of SILAC Mass Spectrometry experiments for protein:protein interactions
Project Status: Code available on request
Soares, D.C., Bradshaw, N.J., Zou, J., Kennaway, C.K., Hamilton, R.S., Chen, Z.A., Wear, M.A., Blackburn, E.A., Bramham, J., Böttcher, B, Millar, J.K., Barlow, P.N., Walkinshaw, M.D., Rappsilber, J., and Porteous, D.J (2012) The mitotic and neurodevelopmentally-critical proteins NDE1 and NDEL1 form dimers, tetramers and polymers with a folded-back structure in solution. JBC[DOI]
RNA2DSearch
A pipeline for searching for defined short RNA secondary structures on a genomic scale.
Hamilton, R.S., Hartswood, E., Jones, C., Vendra, G., Van De Bor, V., Finnegan, D., & Davis, I. (2008) A bioinformatics search pipeline, RNA2DSearch, identifies RNA localization elements in Drosophila retrotransposons. RNA, 15, 200-207. [DOI]
Supplementary Information:
| RNA2DSearch Hits Tables | [txt 15Kb] [txt 6.1Mb] |
| Flybase TE Database | [Release 5.1] [Release 5.12 (Lastest Oct08)] |
| RNAMotif description files | [G2andIwScore][GandI] [GandIwScore] [GandIwScoreUU_CAA] [GandIwScoreUU] [GonlyFixed] [IandG2loose] [IandG2mid] [IandG2tight] [IonlyFixed] [JockeyandIwScore] |
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