Package: SynExtend 1.25.2

Nicholas Cooley

SynExtend: Tools for Comparative Genomics

A multitude of tools for comparative genomics, focused on large-scale analyses of biological data. SynExtend includes tools for working with syntenic data, clustering massive network structures, and estimating functional relationships among genes.

Authors:Nicholas Cooley [aut, cre], Aidan Lakshman [aut, ctb], Adelle Fernando [ctb], Erik Wright [aut]

SynExtend_1.25.2.tar.gz

SynExtend_1.25.2.tgz(r-4.6-x86_64)SynExtend_1.25.2.tgz(r-4.6-arm64)SynExtend_1.25.2.tgz(r-4.5-x86_64)SynExtend_1.25.2.tgz(r-4.5-arm64)
SynExtend_1.25.2.tar.gz(r-4.7-arm64)SynExtend_1.25.2.tar.gz(r-4.7-x86_64)SynExtend_1.25.2.tar.gz(r-4.6-arm64)SynExtend_1.25.2.tar.gz(r-4.6-x86_64)
SynExtend_1.25.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SynExtend/json (API)

# Install 'SynExtend' in R:

install.packages('SynExtend', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/npcooley/synextend/issues

Uses libs:

fortran– Runtime library for GNU Fortran applications
openmp– GCC OpenMP (GOMP) support library

Datasets:

BuiltInEnsembles - Pretrained EvoWeaver Ensemble Models
ExampleStreptomycesData - Example EvoWeaver Input Data from _Streptomyces_ Species
genecalls - Example genecall data
Generic - Model for predicting PID based on k-mer statistics
init_pairs - Example genecall data
linked_features - Example genecall data
syn - Example genecall data

On BioConductor:SynExtend-1.25.2(bioc 3.24)SynExtend-1.24.0(bioc 3.23)

genetics clustering comparativegenomics dataimport fortran openmp

6.06 score 1 stars 85 scripts 38 exports 24 dependencies

Last updated from:8077d0c9fb. Checks:7 NOTE, 2 OK, 2 ERROR, 3 FAIL. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	193
linux-devel-arm64	NOTE	306
linux-devel-x86_64	NOTE	414
source / vignettes	OK	275
linux-release-arm64	NOTE	355
linux-release-x86_64	NOTE	373
macos-release-arm64	NOTE	234
macos-release-x86_64	ERROR	578
macos-oldrel-arm64	NOTE	316
macos-oldrel-x86_64	ERROR	282
windows-devel	FAIL	93
windows-release	FAIL	71
windows-oldrel	FAIL	94
wasm-release	OK	150

Exports:AAHitScoping ApproximateBackground as.simMat BlastSeqs BlockByRank CheckAgainstReport CreateDecoys dendrapply Diag Diag<-DisjointSet DPhyloStatistic EstimateExoLabel EstimRearrScen EvaluatePairs EvoWeaver ExoLabel ExtractBy FastQFromSRR FeaturesFromDF FindSets FitchParsimony FrameDownward GetTranslatedFeatures HitConsensus MakeBlastDb MoranI NormVec NucleotideOverlap OneSite PhyloDistance RandForest SequenceSimilarity simMat SpeciesTree SquaregffBy SummarizePairs SuperTree

Dependencies:BiocGenerics Biostrings bit bit64 blob cachem cli cpp11 crayon DBI DECIPHER fastmap generics glue IRanges lifecycle memoise pkgconfig rlang RSQLite S4Vectors Seqinfo vctrs XVector

Using SynExtend

Introduction | Package Structure | Installation | Usage

Rendered fromUsingSynExtend.Rmdusingknitr::rmarkdown

Last update: 2026-06-18
Started: 2020-02-13

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Adjust the scope of kmer hits between feature and genome space.	AAHitScoping
Return the approximate background alignment score for a series of paired sequences.	ApproximateBackground
Run BLAST queries from R	BlastSeqs
Return simple summaries of blocks of candidate pairs.	BlockByRank
Pretrained EvoWeaver Ensemble Models	BuiltInEnsembles
Pull an assembly from the NCBI FTP site.	CheckAgainstReport
Simulated Null Distributions for CI Distance	CIDist_NullDist
Generating Decoy Alignments for Feature Pairs	CreateDecoys
Decision Trees for Random Forests	as.dendrogram.DecisionTree DecisionTree-class plot.DecisionTree
Apply a Function to All Nodes of a Dendrogram	dendrapply
Return single linkage clusters from 'PairSummaries' objects.	DisjointSet
D-Statistic for Binary States on a Phylogeny	DPhyloStatistic
Estimate ExoLabel Disk Consumption	EstimateExoLabel
Estimate Genome Rearrangement Scenarios with Double Cut and Join Operations	EstimateRearrangementScenarios EstimRearrScen
Evaluating and Filtering Candidate Feature Pairs Against Decoy Alignments	EvaluatePairs
EvoWeaver: Identifying Gene Functional Associations from Coevolutionary Signals	EvoWeaver EvoWeaver-class EvoWeaver-utils SpeciesTree SpeciesTree.EvoWeaver
Gene Organization Predictions for EvoWeaver	EvoWeaver-GOPreds GeneDistance.EvoWeaver MoransI.EvoWeaver OrientationMI.EvoWeaver
Phylogenetic Profiling Predictions for EvoWeaver	Behdenna.EvoWeaver CorrGL.EvoWeaver EvoWeaver-PPPreds ExtantJaccard.EvoWeaver GLDistance.EvoWeaver GLMI.EvoWeaver Hamming.EvoWeaver PAJaccard.EvoWeaver PAOverlap.EvoWeaver ProfDCA.EvoWeaver
Phylogenetic Structure Predictions for EvoWeaver	EvoWeaver-PSPreds RPContextTree.EvoWeaver RPMirrorTree.EvoWeaver TreeDistance.EvoWeaver
Sequence Level Predictions for EvoWeaver	Ancestral.EvoWeaver EvoWeaver-SLPreds GeneVector.EvoWeaver SequenceInfo.EvoWeaver
EvoWeb: Predictions from EvoWeaver	EvoWeb
Example EvoWeaver Input Data from _Streptomyces_ Species	ExampleStreptomycesData
ExoLabel: Out-of-Memory Fast Label Propagation	ExoLabel
Extract and organize 'DNAStringSets's.	ExtractBy
Get Sequencing Data from the SRA	FastQFromSRR
Return a DNAStringSet of features	FeaturesFromDF
Find all single linkage clusters in an undirected pairs list.	FindSets
Calculate ancestral states using Fitch Parsimony	FitchParsimony
Adjust a DataFrame of genecalls	FrameDownward
Example genecall data	genecalls
Model for predicting PID based on k-mer statistics	Generic
Translate Nucleotide Features to Amino Acid Sequences	GetTranslatedFeatures
Return a numeric measure of whether kmer hits linking two genomic features are in linearly similar locations in both features.	HitConsensus
Example genecall data	init_pairs
Example genecall data	linked_features
Tables of where syntenic hits link pairs of genes	LinkedPairs-class print.LinkedPairs [.LinkedPairs
Create a BLAST Database from R	MakeBlastDb
Moran's _I_ Spatial Autocorrelation Index	MoranI
Unit normalize a vector	NormVec
Tabulating Features Linked by Syntenic Hits	NucleotideOverlap
Calculate a site on a right hyperbola.	OneSite
Calculate Distance between Unrooted Phylogenies	PhyloDistance
Clustering Information Distance	CIDist PhyloDistance-CI
Jaccard-Robinson-Foulds Distance and Nye Similarity	JRFDist PhyloDistance-JRF
Kuhner-Felsenstein Distance	KFDist PhyloDistance-KF
Robinson-Foulds Distance	PhyloDistance-RF RFDist
Plot predictions in a EvoWeb object	plot.EvoWeb
Make predictions with EvoWeaver objects	predict.EvoWeaver
Classification and Regression with Random Forests	predict.RandForest RandForest RandForest.fit
Return a numeric value that represents the similarity between two aligned sequences as determined by a provided subsitution matrix.	SequenceSimilarity
Similarity Matrices	as.data.frame.simMat as.matrix.simMat as.simMat as.simMat.matrix as.simMat.vector Diag Diag.simMat Diag<- Diag<-.simMat print.simMat simMat simMat-class
Convert a GRanges object to a DataFrame	SquaregffBy
Subsetting dendrogram objects	subset.dendrogram
Summarizing Linked Feature Pairs from a LinkedPairs Object	SummarizePairs
Create a Species Tree from Gene Trees	SuperTree
Example Dendrograms	SuperTreeEx
Example genecall data	syn
Tabulating Features Linked by Syntenic Hits	ToFeatureSpace