Files in npcooley/SynExtend
Tools for Working With Synteny Objects
.github/workflows/rpkgchecks.yml
.gitignore
DESCRIPTION
NAMESPACE
NEWS.md
R/BlastSeqs.R
R/BlockExpansion.R
R/BlockReconciliation.R
R/ClusterByK.R
R/DPhyloStatistic.R
R/DisjointSet.R
R/EstimRearrScen.R
R/EvoWeaver-GOPreds.R
R/EvoWeaver-PPPreds.R
R/EvoWeaver-PSPreds.R
R/EvoWeaver-SLPreds.R
R/EvoWeaver-class.R
R/EvoWeaver-utils.R
R/EvoWeb-class.R
R/ExoLabel.R
R/ExpandDiagonal.R
R/ExtractBy.R
R/FastDend-class.R
R/FastQFromSRR.R
R/FindSets.R
R/FitchParsimony.R
R/HungarianAssignment.R
R/LanczosEigen.R
R/LinkedPairs-class.R
R/MoranI.R
R/NucleotideOverlap.R
R/PairSummaries.R
R/PhyloDistance.R
R/PrepareSeqs.R
R/RandForest.R
R/SelectByK.R
R/SequenceSimilarity.R
R/ShuffleC.R
R/SubSetPairs.R
R/SummarizePairs.R
R/SuperTree.R
R/dendrapply.R
R/dineof.R
R/gffToDataFrame.R
R/simMat-class.R
R/subset-dendrogram.R
README.md
data/BuiltInEnsembles.RData
data/CIDist_NullDist.RData
data/Endosymbionts_GeneCalls.RData
data/Endosymbionts_LinkedFeatures.RData
data/Endosymbionts_Pairs01.RData
data/Endosymbionts_Pairs02.RData
data/Endosymbionts_Pairs03.RData
data/Endosymbionts_Sets.RData
data/Endosymbionts_Synteny.RData
data/ExampleStreptomycesData.RData
data/Generic.RData
data/SuperTreeEx.RData
data/datalist
inst/extdata/Endosymbionts.sqlite
inst/extdata/Endosymbionts_v02.sqlite
inst/extdata/GCF_021065005.1_ASM2106500v1_genomic.gff.gz
inst/extdata/GCF_023585825.1_ASM2358582v1_genomic.gff.gz
inst/scripts/extdata.R
man/BlastSeqs.Rd
man/BlockExpansion.Rd
man/BlockReconciliation.Rd
man/BuiltInEnsembles.Rd
man/CIDist_NullDist.Rd
man/ClusterByK.Rd
man/DPhyloStatistic.Rd
man/DecisionTree-class.Rd
man/DisjointSet.Rd
man/Endosymbionts_GeneCalls.Rd
man/Endosymbionts_LinkedFeatures.Rd
man/Endosymbionts_Pairs01.Rd
man/Endosymbionts_Pairs02.Rd
man/Endosymbionts_Pairs03.Rd
man/Endosymbionts_Sets.Rd
man/Endosymbionts_Synteny.Rd
man/EstimRearrScen.Rd
man/EstimateExoLabel.Rd
man/EvoWeaver-GOPreds.Rd
man/EvoWeaver-PPPreds.Rd
man/EvoWeaver-PSPreds.Rd
man/EvoWeaver-SLPreds.Rd
man/EvoWeaver.Rd
man/EvoWeb.Rd
man/ExampleStreptomycesData.Rd
man/ExoLabel.Rd
man/ExpandDiagonal.Rd
man/ExtractBy.Rd
man/FastQFromSRR.Rd
man/FindSets.Rd
man/FitchParsimony.Rd
man/Generic.Rd
man/LinkedPairs-class.Rd
man/MakeBlastDb.Rd
man/MoransI.Rd
man/NucleotideOverlap.Rd
man/PairSummaries.Rd
man/PhyloDistance-CI.Rd
man/PhyloDistance-JRF.Rd
man/PhyloDistance-KF.Rd
man/PhyloDistance-RF.Rd
man/PhyloDistance.Rd
man/PrepareSeqs.Rd
man/RandForest.Rd
man/SelectByK.Rd
man/SequenceSimilarity.Rd
man/SubSetPairs.Rd
man/SummarizePairs.Rd
man/SuperTree.Rd
man/SuperTreeEx.Rd
man/dendrapply.Rd
man/gffToDataFrame.Rd
man/plot.EvoWeb.Rd
man/predict.EvoWeaver.Rd
man/simMat.Rd
man/subset-dendrogram.Rd
src/CDend.c
src/CDend.h
src/CShuffle.c
src/HungarianAlgo.c
src/HungarianAlgo.h
src/LoserTree.c
src/LoserTree.h
src/Makevars
src/MoranI.c
src/NucleotideCounts.c
src/OnDiskLP.c
src/PrefixTrie.c
src/PrefixTrie.h
src/R_init_synextend.c
src/RandomForest.c
src/RandomForest.h
src/SEutils.c
src/SEutils.h
src/SynExtend.h
src/XORRand.c
src/_fortran_tabulate.f95
src/_fortran_utils.f95
src/calcMIR2C.c
src/cart_fort.f95
src/dendrapply.c
src/fortran_includes.h
vignettes/UsingSynExtend.Rmd
