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]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SynExtend/json (API)

# 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:

BuiltInEnsembles - Pretrained EvoWeaver Ensemble Models
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
ExampleStreptomycesData - Example EvoWeaver Input Data from _Streptomyces_ Species
Generic - Model for predicting PID based on k-mer statistics

On BioConductor:SynExtend-1.25.4(bioc 3.24)SynExtend-1.24.0(bioc 3.23)

genetics clustering comparativegenomics dataimport fortran openmp

6.00 score 2 stars 84 scripts 494 downloads 44 exports 24 dependencies

Last updated from:417dfcc72b (on RELEASE_3_23). Checks:9 NOTE, 2 OK, 5 FAIL. Indexed: no.

Target	Result	Time
bioc-checks	NOTE	168
linux-devel-arm64	NOTE	342
linux-devel-x86_64	NOTE	486
source / vignettes	OK	216
linux-release-arm64	NOTE	333
linux-release-x86_64	NOTE	439
macos-release-arm64	NOTE	332
macos-release-x86_64	NOTE	481
macos-oldrel-arm64	NOTE	329
macos-oldrel-x86_64	NOTE	497
windows-devel-arm64	FAIL	219
windows-devel-x86_64	FAIL	59
windows-release-arm64	FAIL	177
windows-release-x86_64	FAIL	64
windows-oldrel-x86_64	FAIL	59
wasm-release	OK	115

Exports:AAHitScoping ApproximateBackground as.simMat BlastSeqs BlockByRank BlockExpansion BlockReconciliation CheckAgainstReport ClusterByK CompetePairs dendrapply Diag Diag<-DisjointSet DPhyloStatistic EstimateExoLabel EstimRearrScen EvoWeaver ExoLabel ExpandDiagonal ExtractBy FastQFromSRR FindSets FitchParsimony gffToDataFrame HitConsensus MakeBlastDb MoranI NormVec NucleotideOverlap OneSite PairSummaries PhyloDistance PrepareSeqs RandForest RejectionBy SelectByK SequenceSimilarity simMat SpeciesTree SubSetPairs SummarizePairs SuperTree WithinSetCompetition

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: 2025-03-10
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
Attempt to expand blocks of paired features in a 'PairSummaries' object.	BlockExpansion
Rejection scheme for asyntenic predicted pairs	BlockReconciliation
Pretrained EvoWeaver Ensemble Models	BuiltInEnsembles
Pull an assembly from the NCBI FTP site.	CheckAgainstReport
Simulated Null Distributions for CI Distance	CIDist_NullDist
Predicted pair trimming using K-means.	ClusterByK
Find the best match pair in cases where ambiguity exists.	CompetePairs
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
Example genecalls	Endosymbionts_GeneCalls
Example synteny links	Endosymbionts_LinkedFeatures
Example predicted pairs	Endosymbionts_Pairs01
Example predicted pairs	Endosymbionts_Pairs02
Example predicted pairs	Endosymbionts_Pairs03
A list of disjoint sets.	Endosymbionts_Sets
A synteny object	Endosymbionts_Synteny
Estimate ExoLabel Disk Consumption	EstimateExoLabel
Estimate Genome Rearrangement Scenarios with Double Cut and Join Operations	EstimateRearrangementScenarios EstimRearrScen
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
Attempt to expand blocks of paired features in a 'PairSummaries' object.	ExpandDiagonal
Extract and organize 'DNAStringSets's.	ExtractBy
Get Sequencing Data from the SRA	FastQFromSRR
Find all single linkage clusters in an undirected pairs list.	FindSets
Calculate ancestral states using Fitch Parsimony	FitchParsimony
Model for predicting PID based on k-mer statistics	Generic
Generate a DataFrame of gene calls from a gff3 file	gffToDataFrame
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 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 Pairs of Genomic Sequences	NucleotideOverlap
Calculate a site on a right hyperbola.	OneSite
Summarize connected pairs in a LinkedPairs object	PairSummaries
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
Add feature sequences to Decipher databases.	PrepareSeqs
Classification and Regression with Random Forests	predict.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 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
Subsetting dendrogram objects	subset.dendrogram
Subset a ``PairSummaries'' object.	SubSetPairs
Provide summaries of hypothetical orthologs.	SummarizePairs
Create a Species Tree from Gene Trees	SuperTree
Example Dendrograms	SuperTreeEx
Pare down candidate pairs to one-to-one sets.	WithinSetCompetition