This is a rather random ordered list of the things I have been working on. “One of these days I am going to get myself organazized” and this will have a little bit more structure to it. Most of these links lead to password protected pages, if want access to any of them please ask me.
The idea behind these pages is to try to keep an on-line lab book of the analysis I do. If you work with me on any of these projects and you would like to know the user name and password to gain access to the project pages please ask and I will be happy to give you access.
| Notch Project | Dale Lab | Notch Signalling Project |
| PSM Project | Dale Lab | PSM Clock and Wave Project |
| B. subtilis Project | Stanley Wall Lab | Transposon Mutagenesis Project |
| Phy Tom Project | Huitema Lab | Tomato Phytophera Project |
| Sumo Project | Hay lab | SUMO heat shock Project |
| Hypoxia Project | Rocha Lab | Genome wide Methylation ChIP-seq in hypoxia |
| Yeast RNA-seq | Data Analysis Group | High replicate rna-seq Yeast SNF2 mutant |
| Owen-Hughes Lab | Owen-Hughes Lab | Work on various projects with the TOH lab |
| Chromatin States | Potential project looking at chromatin states in methylation data | |
| Worm SNPs | Gartner Lab | Assisting with variant analysis of C. elegans |
| Great RNA-seq Papers | Barton Lab | Work on the Yeast \(\Delta\)SNF2 papers |
| RNA-seq Normalisation | Barton Lab | Application of SpikeNorm package to two data sets |
| Serratia marcescens | Sargent Lab | ChIP-seq in Serratia marcescens ChiR system |
| Mouse Microarrays | Undergraduate Project | Reexamination of microarray data on mouse gene chip for PKD2 Knockout |
| Bind-n-Seq Project | Ryan Lab | Motif discovery in synthetic DNA protein binding ChIP-seq |
| RBPj | Kim | ChIPseq |
| iPSC | Marios | RNAseq |
| Face recognition | Black Lab (CAHID) | Childhood facial recognition project |
| FtM Faces | C. Wilkinson (CAHID) | The effects of exogenous testosterone on female to male transsexuals |
| BRAF inhibitors | Inman Lab | Illumina BeadArry expression analysis |
| NFE2L2 | Division Cancer Research | Small ChIP-seq analysis for Michael McMahon, in Prof John Hayes’ group |
| SpikeNorm | Data Analysis Group | Documentation for development of the Spike-in Normalisation R package. This package now has a GitHub repository |
| pietalib | Data Analysis Group | Documentation for development of my private functions as an R package called pietalib. This package now has a GitHub repository |
| a4Assemble | Data Analysis Group | Documentation for development of my R package for controlling the a4 assembly pipeline. This package now has a GitHub repository |
| Teaching pages | Teaching pages |
Each project has a specific separate analysis monthly notebook containing the work carried out on that project in detail. The idea is not that these notebooks are able to be run as an automated pipeline to reproduce the complete analysis in one step and regenerate the html, but that all the analysis code is recorded and if necessary it is there and could be repeated. However some of the steps are submissions of jobs to the cluster that produce output. Rather than write complex set of code to manage looking for the existence of intermediate files the notebooks are currently designed to be run piecemeal, to produce the necessary intermediate files. It would be possible to automate this with recursive runs using make I expect but I don’t want to spend time on that.
| Current Month | Current Months Work Log | |
| Work Logs | Records of what I have been working on over the months | |
| Time Sheets | Recording time sheets |
DAG Projects the DAG projects database