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| Atong | Systematic genetic analysis with ordered arrays of yeast deletion Tong et. al. (2004). |
| AtongFnDomain | The functional domains shared by the tested pairs in Tong et al experiment. |
| AtongPair | Data frame the pair of yeast gene tested in Tong et al. 2004. |
| Boeke2006 | Incidence matrix of Synthetic Lethal interaction from the Boeke Lab |
| Boeke2006raw | Incidence matrix of Synthetic Lethal interaction from the Boeke Lab |
| byComplex | Evaluate protein co-membership within cellular organizational units |
| comemberIn | Retrieve the biological complexes. |
| compare | Compare observed data to expected in permutation models |
| compare-method | Compare observed data to expected in permutation models |
| congruence | Calculate congruence score between pairs of of genes sharing pattern of synthetic genetic interactions (Ye et al. (2005)). |
| createSquareMatrix | Create a square matrix |
| domainDist | Finds the number of gene sets for each shared domain |
| dSLAM | dSLAM platform used for Synthetic Lethal screens in the Boeke Lab |
| dSLAM.GPL1444 | dSLAM platform used for Synthetic Lethal screens in the Boeke Lab |
| essglist | The list of yeast essential genes |
| getAlignStats | Functions to do local alignment of two sequences using EMBOSS matcher |
| getInteraction | Count genetic interactions within and between cellular organizational units |
| getSharedDomains | Find domains shared by a given list of gene names. |
| getSharedInteraction | Calculate the number of shared synthetic genetic interactions between pairs of genes. |
| getTestedPairs | Find interacting and non-interacting tested pairs from an genetic interaction matrix. |
| getUniquePairs | Find unique pairs from an genetic interaction matrix. |
| gi2005 | Genetic Interaction Data (EMAP) from the yeast early secretory pathway |
| gi2005.metadata | Genetic Interaction Data (EMAP) from the yeast early secretory pathway |
| gi2007 | Synthetic Genetic Interaction data from Collins et al |
| gi2007.metadata | Synthetic Genetic Interaction data from Collins et al |
| gi2Interactome | Reduce genetic interactions matrix |
| hyperG | Hypergeometric test |
| iSummary | Summarize cellular organizational units sharing genetic interaction |
| modelSLGI | Permutation model for assessing synthetic genetic interactions in cellular organizational units. |
| normInteraction | Normalize a matrix of biological interactions |
| plot | Graphical method to represent the result of the modelSLGI . |
| plot-method | Graphical method to represent the result of the modelSLGI . |
| SDL | The Association matrix for the synthetic dosage lethal screens in Yeast. |
| seqMatcherAlign | Functions to do local alignment of two sequences using EMBOSS matcher |
| SGA | Systematic genetic analysis with ordered arrays of yeast deletion. |
| SGAraw | Systematic genetic analysis with ordered arrays of yeast deletion. |
| SGD.SL | Interaction data from the Saccharomyces Genome Database |
| SGD.SynGrowthDefect | Interaction data from the Saccharomyces Genome Database |
| SGD.SynRescue | Interaction data from the Saccharomyces Genome Database |
| sharedBy | Find the gene pairs that share a domain. |
| sharedInt | List shared genetic interactions between genes |
| show-method | A class for representing the result of the SLGI graph permutation model. |
| siResult-class | A class for representing the result of the SLGI graph permutation model. |
| SLchr | The Association matrix for the synthetic dosage lethal screens in Yeast. |
| test2Interact | Summarize genetic interactions within or between cellular organizational units |
| TFmat | Transcription Factor Binding Affinities |
| tong2004raw | Systematic genetic analysis with ordered arrays of yeast deletion Tong et. al. (2004). |
| topInteraction | Extract interacting biological complexes |
| twoWayTable | Generate two-way table for genetic interaction data |
| withinComplex | Search for protein co-membership within complexes. |