as.data.frame.simMat | Similarity Matrices |
as.matrix.simMat | Similarity Matrices |
as.simMat | Similarity Matrices |
as.simMat.matrix | Similarity Matrices |
as.simMat.vector | Similarity Matrices |
Behdenna.ProtWeaver | Presence/Absence Predictions for ProtWeaver |
BlastSeqs | Run BLAST queries from R |
BlockExpansion | Attempt to expand blocks of paired features in a 'PairSummaries' object. |
BlockReconciliation | Rejection scheme for asyntenic predicted pairs |
BuiltInEnsembles | Pretrained ProtWeaver Ensemble Models |
Coloc.ProtWeaver | Co-localization Predictions for ProtWeaver |
ContextTree.ProtWeaver | Distance Matrix Predictions for ProtWeaver |
Diag | Similarity Matrices |
Diag.simMat | Similarity Matrices |
Diag<- | Similarity Matrices |
Diag<-.simMat | Similarity Matrices |
DisjointSet | Return single linkage clusters from 'PairSummaries' objects. |
DPhyloStatistic | D-Statistic for Binary States on a Phylogeny |
Endosymbionts_GeneCalls | Example genecalls |
Endosymbionts_LinkedFeatures | Example synteny links |
Endosymbionts_Pairs01 | Example predicted pairs |
Endosymbionts_Pairs02 | Example predicted pairs |
Endosymbionts_Pairs03 | Example predicted pairs |
Endosymbionts_Sets | A list of disjoint sets. |
Endosymbionts_Synteny | A synteny object |
EstimateRearrangementScenarios | Estimate Genome Rearrangement Events with Double Cut and Join Operations |
EstimRearrScen | Estimate Genome Rearrangement Events with Double Cut and Join Operations |
ExampleStreptomycesData | Example ProtWeaver Input Data from _Streptomyces_ Species |
ExtractBy | Extract and organize 'DNAStringSets's. |
FindSets | Find all single linkage clusters in an undirected pairs list. |
GainLoss.ProtWeaver | Presence/Absence Predictions for ProtWeaver |
GeneralizedRF | Information-Theoretic Generalized Robinson-Foulds Distance |
Generic | Model for predicting PID based on k-mer statistics |
gffToDataFrame | Generate a DataFrame of gene calls from a gff3 file |
Hamming.ProtWeaver | Presence/Absence Predictions for ProtWeaver |
Jaccard.ProtWeaver | Presence/Absence Predictions for ProtWeaver |
LinkedPairs-class | Tables of where syntenic hits link pairs of genes |
MirrorTree.ProtWeaver | Distance Matrix Predictions for ProtWeaver |
MutualInformation.ProtWeaver | Presence/Absence Predictions for ProtWeaver |
NucleotideOverlap | Tabulating Pairs of Genomic Sequences |
PairSummaries | Summarize connected pairs in a LinkedPairs object |
plot.ProtWeb | Plot predictions in a ProtWeb object |
predict.ProtWeaver | Make predictions with ProtWeaver objects |
print.LinkedPairs | Tables of where syntenic hits link pairs of genes |
print.simMat | Similarity Matrices |
ProfDCA.ProtWeaver | Presence/Absence Predictions for ProtWeaver |
ProtWeaver | ProtWeaver: Predicting Protein Functional Association Networks |
ProtWeaver-class | ProtWeaver: Predicting Protein Functional Association Networks |
ProtWeaver-ColocPreds | Co-localization Predictions for ProtWeaver |
ProtWeaver-DMPreds | Distance Matrix Predictions for ProtWeaver |
ProtWeaver-PAPreds | Presence/Absence Predictions for ProtWeaver |
ProtWeaver-ResiduePreds | Residue Based Predictions for ProtWeaver |
ProtWeaver-utils | ProtWeaver: Predicting Protein Functional Association Networks |
ProtWeb | ProtWeb: Predictions from ProtWeaver |
ResidueMI.ProtWeaver | Residue Based Predictions for ProtWeaver |
RFDist | Robinson-Foulds Distance |
SelectByK | Predicted pair trimming using K-means. |
SequenceSimilarity | Return a numeric value that represents the similarity between two aligned sequences as determined by a provided subsitution matrix. |
simMat | Similarity Matrices |
simMat-class | Similarity Matrices |
SubSetPairs | Subset a "PairSummaries" object. |
SuperTree | Create a Species Tree from Gene Trees |
SuperTreeEx | Example Dendrograms |
[.LinkedPairs | Tables of where syntenic hits link pairs of genes |