Package: SynExtend 1.24.0

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_1.24.0.tar.gz

SynExtend_1.24.0.tgz(r-4.6-x86_64)SynExtend_1.24.0.tgz(r-4.6-arm64)SynExtend_1.24.0.tgz(r-4.5-x86_64)SynExtend_1.24.0.tgz(r-4.5-arm64)
SynExtend_1.24.0.tar.gz(r-4.7-arm64)SynExtend_1.24.0.tar.gz(r-4.7-x86_64)SynExtend_1.24.0.tar.gz(r-4.6-arm64)SynExtend_1.24.0.tar.gz(r-4.6-x86_64)
SynExtend_1.24.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
SynExtend/json (API)
NEWS

# Install 'SynExtend' in R:
install.packages('SynExtend', repos = c('https://bioc-release.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:

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

geneticsclusteringcomparativegenomicsdataimportfortranopenmp

5.80 score 1 stars 85 scripts 385 downloads 44 exports 24 dependencies

Last updated from:417dfcc72b (on RELEASE_3_23). Checks:7 NOTE, 2 OK, 2 ERROR, 3 FAIL. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE189
linux-devel-arm64NOTE382
linux-devel-x86_64NOTE397
source / vignettesOK248
linux-release-arm64NOTE375
linux-release-x86_64NOTE426
macos-release-arm64NOTE261
macos-release-x86_64ERROR312
macos-oldrel-arm64NOTE281
macos-oldrel-x86_64ERROR452
windows-develFAIL58
windows-releaseFAIL55
windows-oldrelFAIL65
wasm-releaseOK118

Exports:AAHitScopingApproximateBackgroundas.simMatBlastSeqsBlockByRankBlockExpansionBlockReconciliationCheckAgainstReportClusterByKCompetePairsdendrapplyDiagDiag<-DisjointSetDPhyloStatisticEstimateExoLabelEstimRearrScenEvoWeaverExoLabelExpandDiagonalExtractByFastQFromSRRFindSetsFitchParsimonygffToDataFrameHitConsensusMakeBlastDbMoranINormVecNucleotideOverlapOneSitePairSummariesPhyloDistancePrepareSeqsRandForestRejectionBySelectByKSequenceSimilaritysimMatSpeciesTreeSubSetPairsSummarizePairsSuperTreeWithinSetCompetition

Dependencies:BiocGenericsBiostringsbitbit64blobcachemclicpp11crayonDBIDECIPHERfastmapgenericsglueIRangeslifecyclememoisepkgconfigrlangRSQLiteS4VectorsSeqinfovctrsXVector

Using SynExtend

Nicholas Cooley

Rendered fromUsingSynExtend.Rmdusingknitr::rmarkdownon Jun 15 2026.

Last update: 2025-03-10
Started: 2020-02-13

Readme and manuals

Help Manual

Help pageTopics
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 RBlastSeqs
Return simple summaries of blocks of candidate pairs.BlockByRank
Attempt to expand blocks of paired features in a 'PairSummaries' object.BlockExpansion
Rejection scheme for asyntenic predicted pairsBlockReconciliation
Pretrained EvoWeaver Ensemble ModelsBuiltInEnsembles
Pull an assembly from the NCBI FTP site.CheckAgainstReport
Simulated Null Distributions for CI DistanceCIDist_NullDist
Predicted pair trimming using K-means.ClusterByK
Find the best match pair in cases where ambiguity exists.CompetePairs
Decision Trees for Random Forestsas.dendrogram.DecisionTree DecisionTree-class plot.DecisionTree
Apply a Function to All Nodes of a Dendrogramdendrapply
Return single linkage clusters from 'PairSummaries' objects.DisjointSet
D-Statistic for Binary States on a PhylogenyDPhyloStatistic
Example genecallsEndosymbionts_GeneCalls
Example synteny linksEndosymbionts_LinkedFeatures
Example predicted pairsEndosymbionts_Pairs01
Example predicted pairsEndosymbionts_Pairs02
Example predicted pairsEndosymbionts_Pairs03
A list of disjoint sets.Endosymbionts_Sets
A synteny objectEndosymbionts_Synteny
Estimate ExoLabel Disk ConsumptionEstimateExoLabel
Estimate Genome Rearrangement Scenarios with Double Cut and Join OperationsEstimateRearrangementScenarios EstimRearrScen
EvoWeaver: Identifying Gene Functional Associations from Coevolutionary SignalsEvoWeaver EvoWeaver-class EvoWeaver-utils SpeciesTree SpeciesTree.EvoWeaver
Gene Organization Predictions for EvoWeaverEvoWeaver-GOPreds GeneDistance.EvoWeaver MoransI.EvoWeaver OrientationMI.EvoWeaver
Phylogenetic Profiling Predictions for EvoWeaverBehdenna.EvoWeaver CorrGL.EvoWeaver EvoWeaver-PPPreds ExtantJaccard.EvoWeaver GLDistance.EvoWeaver GLMI.EvoWeaver Hamming.EvoWeaver PAJaccard.EvoWeaver PAOverlap.EvoWeaver ProfDCA.EvoWeaver
Phylogenetic Structure Predictions for EvoWeaverEvoWeaver-PSPreds RPContextTree.EvoWeaver RPMirrorTree.EvoWeaver TreeDistance.EvoWeaver
Sequence Level Predictions for EvoWeaverAncestral.EvoWeaver EvoWeaver-SLPreds GeneVector.EvoWeaver SequenceInfo.EvoWeaver
EvoWeb: Predictions from EvoWeaverEvoWeb
Example EvoWeaver Input Data from _Streptomyces_ SpeciesExampleStreptomycesData
ExoLabel: Out-of-Memory Fast Label PropagationExoLabel
Attempt to expand blocks of paired features in a 'PairSummaries' object.ExpandDiagonal
Extract and organize 'DNAStringSets's.ExtractBy
Get Sequencing Data from the SRAFastQFromSRR
Find all single linkage clusters in an undirected pairs list.FindSets
Calculate ancestral states using Fitch ParsimonyFitchParsimony
Model for predicting PID based on k-mer statisticsGeneric
Generate a DataFrame of gene calls from a gff3 filegffToDataFrame
Return a numeric measure of whether kmer hits linking two genomic features are in linearly similar locations in both features.HitConsensus
Tables of where syntenic hits link pairs of genesLinkedPairs-class print.LinkedPairs [.LinkedPairs
Create a BLAST Database from RMakeBlastDb
Moran's _I_ Spatial Autocorrelation IndexMoranI
Unit normalize a vectorNormVec
Tabulating Pairs of Genomic SequencesNucleotideOverlap
Calculate a site on a right hyperbola.OneSite
Summarize connected pairs in a LinkedPairs objectPairSummaries
Calculate Distance between Unrooted PhylogeniesPhyloDistance
Clustering Information DistanceCIDist PhyloDistance-CI
Jaccard-Robinson-Foulds Distance and Nye SimilarityJRFDist PhyloDistance-JRF
Kuhner-Felsenstein DistanceKFDist PhyloDistance-KF
Robinson-Foulds DistancePhyloDistance-RF RFDist
Plot predictions in a EvoWeb objectplot.EvoWeb
Make predictions with EvoWeaver objectspredict.EvoWeaver
Add feature sequences to Decipher databases.PrepareSeqs
Classification and Regression with Random Forestspredict.RandForest RandForest RandForest.fit
Given an object of candidate pairs, reject false positives.RejectionBy
Predicted pair trimming using K-means.SelectByK
Return a numeric value that represents the similarity between two aligned sequences as determined by a provided subsitution matrix.SequenceSimilarity
Similarity Matricesas.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
Subsetting dendrogram objectssubset.dendrogram
Subset a ``PairSummaries'' object.SubSetPairs
Provide summaries of hypothetical orthologs.SummarizePairs
Create a Species Tree from Gene TreesSuperTree
Example DendrogramsSuperTreeEx
Pare down candidate pairs to one-to-one sets.WithinSetCompetition