Package: treediff 0.2.1
Nathalie Vialaneix
treediff: Testing Differences Between Families of Trees
Perform test to detect differences in structure between families of trees. The method is based on cophenetic distances and aggregated Student's tests.
Authors:
treediff_0.2.1.tar.gz
treediff_0.2.1.tar.gz(r-4.5-noble)treediff_0.2.1.tar.gz(r-4.4-noble)
treediff_0.2.1.tgz(r-4.4-emscripten)treediff_0.2.1.tgz(r-4.3-emscripten)
treediff.pdf |treediff.html✨
treediff/json (API)
NEWS
| # Install 'treediff' in R: |
| install.packages('treediff', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 9 months agofrom:7aefbca0b7. Checks:OK: 1 WARNING: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 14 2024 |
| R-4.5-linux | WARNING | Nov 14 2024 |
Exports:clusterTreeHiC2TreeHiCDOCDataSetnormalizeCounttreediff
Dependencies:abindadjclustaggregationaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitopsbriocalibratecallrcapusheclicodetoolscolorspacecowplotcpp11crayoncsawcurldata.tableDelayedArraydendextenddescdiffobjdigestdplyredgeRevaluatefansifarverformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegridExtragtablegtoolsHiCcompareHiCDOChttrInteractionSetIRangesisobandjsonliteKernSmoothlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmetapodmgcvmimemultiHiCcomparemunsellnlmeopensslpbapplypheatmappillarpkgbuildpkgconfigpkgloadplyrpraiseprocessxpspurrrqqmanR6RColorBrewerRcppRcppArmadilloreshape2rhdf5rhdf5filtersRhdf5libRhtslibrlangrprojrootRsamtoolsS4ArraysS4VectorsscalessnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsystestthattibbletidyselectUCSC.utilsutf8vctrsviridisviridisLitewaldowithrXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Create hierarchical clustering trees for each cluster in a given matrix | clusterTree |
| Convert Hi-C to trees | HiC2Tree |
| Create a HiCDOCDataSet object from a set of files | HiCDOCDataSet |
| Normalize count matrix using cyclic loess | normalizeCount |
| Perform the treediff test | print.treeTest summary.treeTest treediff |