Tools for Comparative Genomics

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Documentation for package ‘SynExtend’ version 1.25.1

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

Help Pages

A B C D E F G H I J K L M N O P R S T misc

-- A --

AAHitScoping	Adjust the scope of kmer hits between feature and genome space.
Ancestral.EvoWeaver	Sequence Level Predictions for EvoWeaver
ApproximateBackground	Return the approximate background alignment score for a series of paired sequences.
as.data.frame.simMat	Similarity Matrices
as.dendrogram.DecisionTree	Decision Trees for Random Forests
as.matrix.simMat	Similarity Matrices
as.simMat	Similarity Matrices
as.simMat.matrix	Similarity Matrices
as.simMat.vector	Similarity Matrices

-- B --

Behdenna.EvoWeaver	Phylogenetic Profiling Predictions for EvoWeaver
BlastSeqs	Run BLAST queries from R
BlockByRank	Return simple summaries of blocks of candidate pairs.
BuiltInEnsembles	Pretrained EvoWeaver Ensemble Models

-- C --

CheckAgainstReport	Pull an assembly from the NCBI FTP site.
CIDist	Clustering Information Distance
CIDist_NullDist	Simulated Null Distributions for CI Distance
CorrGL.EvoWeaver	Phylogenetic Profiling Predictions for EvoWeaver
CreateDecoys	Generating Decoy Alignments for Feature Pairs

-- D --

DecisionTree-class	Decision Trees for Random Forests
dendrapply	Apply a Function to All Nodes of a Dendrogram
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

-- E --

EstimateExoLabel	Estimate ExoLabel Disk Consumption
EstimateRearrangementScenarios	Estimate Genome Rearrangement Scenarios with Double Cut and Join Operations
EstimRearrScen	Estimate Genome Rearrangement Scenarios with Double Cut and Join Operations
EvaluatePairs	Evaluating and Filtering Candidate Feature Pairs Against Decoy Alignments
EvoWeaver	EvoWeaver: Identifying Gene Functional Associations from Coevolutionary Signals
EvoWeaver-class	EvoWeaver: Identifying Gene Functional Associations from Coevolutionary Signals
EvoWeaver-GOPreds	Gene Organization Predictions for EvoWeaver
EvoWeaver-PPPreds	Phylogenetic Profiling Predictions for EvoWeaver
EvoWeaver-PSPreds	Phylogenetic Structure Predictions for EvoWeaver
EvoWeaver-SLPreds	Sequence Level Predictions for EvoWeaver
EvoWeaver-utils	EvoWeaver: Identifying Gene Functional Associations from Coevolutionary Signals
EvoWeb	EvoWeb: Predictions from EvoWeaver
ExampleStreptomycesData	Example EvoWeaver Input Data from _Streptomyces_ Species
ExoLabel	ExoLabel: Out-of-Memory Fast Label Propagation
ExtantJaccard.EvoWeaver	Phylogenetic Profiling Predictions for EvoWeaver
ExtractBy	Extract and organize 'DNAStringSets's.

-- F --

FastQFromSRR	Get Sequencing Data from the SRA
FeaturesFromDF	Return a DNAStringSet of features
FindSets	Find all single linkage clusters in an undirected pairs list.
FitchParsimony	Calculate ancestral states using Fitch Parsimony
FrameDownward	Adjust a DataFrame of genecalls

-- G --

genecalls	Example genecall data
GeneDistance.EvoWeaver	Gene Organization Predictions for EvoWeaver
Generic	Model for predicting PID based on k-mer statistics
GeneVector.EvoWeaver	Sequence Level Predictions for EvoWeaver
GetTranslatedFeatures	Translate Nucleotide Features to Amino Acid Sequences
GLDistance.EvoWeaver	Phylogenetic Profiling Predictions for EvoWeaver
GLMI.EvoWeaver	Phylogenetic Profiling Predictions for EvoWeaver

-- H --

Hamming.EvoWeaver	Phylogenetic Profiling Predictions for EvoWeaver
HitConsensus	Return a numeric measure of whether kmer hits linking two genomic features are in linearly similar locations in both features.

-- I --

init_pairs

Example genecall data

-- J --

JRFDist

Jaccard-Robinson-Foulds Distance and Nye Similarity

-- K --

KFDist

Kuhner-Felsenstein Distance

-- L --

LinkedPairs-class	Tables of where syntenic hits link pairs of genes
linked_features	Example genecall data

-- M --

MakeBlastDb	Create a BLAST Database from R
MoranI	Moran's _I_ Spatial Autocorrelation Index
MoransI.EvoWeaver	Gene Organization Predictions for EvoWeaver

-- N --

NormVec	Unit normalize a vector
NucleotideOverlap	Tabulating Features Linked by Syntenic Hits

-- O --

OneSite	Calculate a site on a right hyperbola.
OrientationMI.EvoWeaver	Gene Organization Predictions for EvoWeaver

-- P --

PAJaccard.EvoWeaver	Phylogenetic Profiling Predictions for EvoWeaver
PAOverlap.EvoWeaver	Phylogenetic Profiling Predictions for EvoWeaver
PhyloDistance	Calculate Distance between Unrooted Phylogenies
PhyloDistance-CI	Clustering Information Distance
PhyloDistance-JRF	Jaccard-Robinson-Foulds Distance and Nye Similarity
PhyloDistance-KF	Kuhner-Felsenstein Distance
PhyloDistance-RF	Robinson-Foulds Distance
plot.DecisionTree	Decision Trees for Random Forests
plot.EvoWeb	Plot predictions in a EvoWeb object
predict.EvoWeaver	Make predictions with EvoWeaver objects
predict.RandForest	Classification and Regression with Random Forests
print.LinkedPairs	Tables of where syntenic hits link pairs of genes
print.simMat	Similarity Matrices
ProfDCA.EvoWeaver	Phylogenetic Profiling Predictions for EvoWeaver

-- R --

RandForest	Classification and Regression with Random Forests
RandForest.fit	Classification and Regression with Random Forests
RFDist	Robinson-Foulds Distance
RPContextTree.EvoWeaver	Phylogenetic Structure Predictions for EvoWeaver
RPMirrorTree.EvoWeaver	Phylogenetic Structure Predictions for EvoWeaver

-- S --

SequenceInfo.EvoWeaver	Sequence Level Predictions for EvoWeaver
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
SpeciesTree	EvoWeaver: Identifying Gene Functional Associations from Coevolutionary Signals
SpeciesTree.EvoWeaver	EvoWeaver: Identifying Gene Functional Associations from Coevolutionary Signals
SquaregffBy	Convert a GRanges object to a DataFrame
subset.dendrogram	Subsetting dendrogram objects
SummarizePairs	Summarizing Linked Feature Pairs from a LinkedPairs Object
SuperTree	Create a Species Tree from Gene Trees
SuperTreeEx	Example Dendrograms
syn	Example genecall data

-- T --

ToFeatureSpace	Tabulating Features Linked by Syntenic Hits
TreeDistance.EvoWeaver	Phylogenetic Structure Predictions for EvoWeaver

-- misc --

[.LinkedPairs

Tables of where syntenic hits link pairs of genes