Tools for Working With Synteny Objects


[Up] [Top]

Documentation for package ‘SynExtend’ version 1.10.2

Help Pages

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