Package: SynExtend 1.17.0
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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:
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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')) |
- BuiltInEnsembles - Pretrained EvoWeaver Ensemble Models
- CIDist_NullDist - Simulated Null Distributions for CI Distance
- 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
- SuperTreeEx - Example Dendrograms
On BioConductor:SynExtend-1.17.0(bioc 3.20)SynExtend-1.16.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:7cdfb94aa8
Exports:as.simMatBlastSeqsBlockExpansionBlockReconciliationClusterByKdendrapplyDiagDiag<-DisjointSetDPhyloStatisticEstimateExoLabelEstimRearrScenEvoWeaverExoLabelExpandDiagonalExtractByFastQFromSRRFindSetsFitchParsimonygffToDataFrameMakeBlastDbMoransINucleotideOverlapPairSummariesPhyloDistancePrepareSeqsSelectByKSequenceSimilaritysimMatSpeciesTreeSubSetPairsSummarizePairsSuperTree
Dependencies:askpassBiocGenericsBiostringsbitbit64blobcachemclicpp11crayoncurlDBIDECIPHERfastmapGenomeInfoDbGenomeInfoDbDatagluehttrIRangesjsonlitelifecyclememoisemimeopensslpkgconfigplogrR6rlangRSQLiteS4VectorssysUCSC.utilsvctrsXVectorzlibbioc