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:Nathalie Vialaneix [aut, cre], Gwendaelle Cardenas [aut], Marie Chavent [aut], Sylvain Foissac [aut], Pierre Neuvial [aut], Nathanael Randriamihamison [aut]

treediff_0.2.1.tar.gz
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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.

5 exports 0.00 score 120 dependencies 263 downloads

Last updated 7 months agofrom:7aefbca0b7. Checks:OK: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 15 2024
R-4.5-linux	OK	Sep 15 2024

Exports:clusterTree HiC2Tree HiCDOCDataSet normalizeCount treediff

Dependencies:abind adjclust aggregation askpass BH Biobase BiocGenerics BiocParallel Biostrings bitops brio calibrate callr capushe cli codetools colorspace cowplot cpp11 crayon csaw curl data.table DelayedArray dendextend desc diffobj digest dplyr edgeR evaluate fansi farver formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gridExtra gtable gtools HiCcompare HiCDOC httr InteractionSet IRanges isoband jsonlite KernSmooth labeling lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats metapod mgcv mime multiHiCcompare munsell nlme openssl pbapply pheatmap pillar pkgbuild pkgconfig pkgload plyr praise processx ps purrr qqman R6 RColorBrewer Rcpp RcppArmadillo rematch2 reshape2 rhdf5 rhdf5filters Rhdf5lib Rhtslib rlang rprojroot Rsamtools S4Arrays S4Vectors scales snow SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment sys testthat tibble tidyselect UCSC.utils utf8 vctrs viridis viridisLite waldo withr XVector zlibbioc

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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

Package: treediff 0.2.1

treediff: Testing Differences Between Families of Trees

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)