- CNAnorm
an R package to perform normalisation of copy number from next
generation sequence data, taking into account tumour cell content and
possible aneuploid genome size. The R package is hosted in the Leeds
Institute of Molecular Medicine server (clicking the link will direct
you there).
- (Old package) MLME
an R package to perform analysis on microarray data using linear
mixture mixed model. Please be advised that the package is currently in
old format, and will be updated.
- CNALR
an R package to stratify tumour subtypes based on copy number alteration profiles using next-generation sequence data (in multiple samples or sequences). The input used in this analysis is the output from CNAnorm package above.
- CNAseg
an R package to perform segmentation of copy number alteration data using the tail-greedy unbalanced Haar wavelet.
- SSCox
an R package to perform survival analysis of patients based on genomic profiles using a novel sparse-smothed Cox proportional hazard model. The input used in this analysis is the output from CNAnorm package above.
- NGSoptwin an R package to estimate the optimal window size in the analysis of very low coverage next-generation sequence data.
- Atest an R package to perform two-sample test on the equivalence of distribution.
- NGStests an R package to perform statistical tests on ChIP-seq data based on next-generation sequencing. The objective is to identify regions that have differential binding in a two-sample setting.

For the Introduction to R course, click here.