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 |
getFASTAname |
Obtain sequence name from FASTA object |
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. |