Package: SynExtend 1.19.0

Nicholas Cooley

SynExtend: Tools for Working With Synteny Objects

Shared order between genomic sequences provide a great deal of information. Synteny objects produced by the R package DECIPHER provides quantitative information about that shared order. SynExtend provides tools for extracting information from Synteny objects.

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

SynExtend_1.19.0.tar.gz
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SynExtend.pdf |SynExtend.html✨
SynExtend/json (API)
NEWS

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

Peer review:

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-1.19.0(bioc 3.21)SynExtend-1.18.0(bioc 3.20)

geneticsclusteringcomparativegenomicsdataimportfortranopenmp

6.23 score 1 stars 70 scripts 160 downloads 34 exports 36 dependencies

Last updated 18 days agofrom:fbefdf6ba8. Checks:OK: 1 NOTE: 5 WARNING: 3. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 04 2024
R-4.5-win-x86_64NOTEDec 04 2024
R-4.5-linux-x86_64NOTEDec 04 2024
R-4.4-win-x86_64NOTEDec 04 2024
R-4.4-mac-x86_64NOTEDec 04 2024
R-4.4-mac-aarch64NOTEDec 04 2024
R-4.3-win-x86_64WARNINGSep 28 2024
R-4.3-mac-x86_64WARNINGSep 28 2024
R-4.3-mac-aarch64WARNINGSep 28 2024

Exports:as.simMatBlastSeqsBlockExpansionBlockReconciliationClusterByKdendrapplyDiagDiag<-DisjointSetDPhyloStatisticEstimateExoLabelEstimRearrScenEvoWeaverExoLabelExpandDiagonalExtractByFastQFromSRRFindSetsFitchParsimonygffToDataFrameMakeBlastDbMoranINucleotideOverlapPairSummariesPhyloDistancePrepareSeqsRandForestSelectByKSequenceSimilaritysimMatSpeciesTreeSubSetPairsSummarizePairsSuperTree

Dependencies:askpassBiocGenericsBiostringsbitbit64blobcachemclicpp11crayoncurlDBIDECIPHERfastmapgenericsGenomeInfoDbGenomeInfoDbDatagluehttrIRangesjsonlitelifecyclememoisemimeopensslpkgconfigplogrR6rlangRSQLiteS4VectorssysUCSC.utilsvctrsXVectorzlibbioc

Using SynExtend

Nicholas Cooley

Rendered fromUsingSynExtend.Rmdusingknitr::rmarkdownon Dec 04 2024.

Last update: 2024-04-25
Started: 2020-02-13

Readme and manuals

Help Manual

Help pageTopics
Run BLAST queries from RBlastSeqs
Attempt to expand blocks of paired features in a 'PairSummaries' object.BlockExpansion
Rejection scheme for asyntenic predicted pairsBlockReconciliation
Pretrained EvoWeaver Ensemble ModelsBuiltInEnsembles
Simulated Null Distributions for CI DistanceCIDist_NullDist
Predicted pair trimming using K-means.ClusterByK
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 Events with Double Cut and Join OperationsEstimateRearrangementScenarios EstimRearrScen
EvoWeaver: Predicting Protein Functional Association NetworksEvoWeaver 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
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
Tabulating Pairs of Genomic SequencesNucleotideOverlap
Summarize connected pairs in a LinkedPairs objectPairSummaries
Calculate Distance between Unrooted PhylogeniesPhyloDistance
Clustering Information DistanceCIDist PhyloDistance-CI
Jaccard-Robinson-Foulds DistanceJRFDist 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
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