iCAGES (integrated CAncer GEnome Score) is an effective tool for prioritizing cancer driver genes for a patient. Given his/her genomic mutation information, iCAGES can accurately prioritize a list of candidate cancer driver genes.
Annokey is a command line tool for annotating gene lists with the results of a key-term search of the NCBI Gene database and linked PubMed article abstracts. Its purpose is to help users prioritise genes by relevance to a domain of interest, such as “breast cancer” or “DNA repair” etcetera. The user steers the search by specifying a ranked list of keywords and terms that are likely to be highly correlated with their domain of interest.
Pan-Tetris is our interactive software tool that enables the visual inspection of gene occurrences in a pan-genome table. It allows the user to modify the composition of such pan gene groups with an aggregation technique that is inspired by the famous Tetris game.
GCUA (General Codon Usage Analysis) is designed to perform various tasks that are of use for evaluating codon usage in a set of genes. You can get it to do some simple things like calculate the number of observations of a particular codon in a gene. Or you can do the same thing for the combined dataset. You can also look at amino acid usage frequencies (again for each gene or for the dataset as a whole). The program also produces a distance matrix based on the similarity of codon usage in genes.
gespeR estimates gene-specific phenotypes from off-target confounded RNAi screens. Observed phenotype for a specfic siRNA is modeled as a linear combination of gene-specific phenotypes from the on- and all off-target genes.