Package: TTMap 1.35.0

Rachel Jeitziner

TTMap: Two-Tier Mapper: a clustering tool based on topological data analysis

TTMap is a clustering method that groups together samples with the same deviation in comparison to a control group. It is specially useful when the data is small. It is parameter free.

Authors:Rachel Jeitziner

TTMap_1.35.0.tar.gz
TTMap_1.35.0.zip(r-4.7)TTMap_1.35.0.zip(r-4.6)TTMap_1.35.0.zip(r-4.5)
TTMap_1.35.0.tgz(r-4.6-any)TTMap_1.35.0.tgz(r-4.5-any)
TTMap_1.35.0.tar.gz(r-4.7-any)TTMap_1.35.0.tar.gz(r-4.6-any)
TTMap_1.35.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
TTMap/json (API)

# Install 'TTMap' in R:

install.packages('TTMap', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:TTMap-1.35.0(bioc 3.24)TTMap-1.34.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

software microarray differentialexpression multiplecomparison clustering classification

4.00 score 3 scripts 380 downloads 1 mentions 15 exports 46 dependencies

Last updated from:d2b271c7bb. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	216
linux-devel-x86_64	NOTE	371
source / vignettes	OK	327
linux-release-x86_64	NOTE	326
macos-release-arm64	NOTE	232
macos-oldrel-arm64	NOTE	171
windows-devel	NOTE	233
windows-release	NOTE	190
windows-oldrel	NOTE	226
wasm-release	OK	158

Exports:calcul_e calcul_e_single control_adjustment generate_correlation generate_euclidean generate_mismatch_distance generate_p_val_correlation generate_single_cell_complete_mismatch generate_single_cell_mismatch_with_parameter hyperrectangle_deviation_assessment make_matrices read_pcl ttmap ttmap_sgn_genes write_pcl

Dependencies:abind base64enc Biobase BiocGenerics bslib cachem cli colorRamps DelayedArray digest evaluate fastmap fontawesome fs generics GenomicRanges highr htmltools htmlwidgets IRanges jquerylib jsonlite knitr lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime R6 rappdirs rgl rlang rmarkdown S4Arrays S4Vectors sass Seqinfo SparseArray SummarizedExperiment tinytex xfun XVector yaml

Manual for the TTMap library

Rendered fromTTMap.Rnwusingutils::Sweaveon May 30 2026.

Last update: 2018-02-27
Started: 2017-11-22

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Two-Tier Mapper: a clustering tool based on topological data analysis	TTMap-package TTMap
Calculation of the value of epsilon	calcul_e calcul_e_single
Calculates a corrected control group, discovers outliers in it.	control_adjustment
Generates different distance matrices	generate_correlation generate_euclidean generate_mismatch_distance generate_p_val_correlation generate_single_cell_complete_mismatch generate_single_cell_mismatch_with_parameter
Calculation of deviation components	hyperrectangle_deviation_assessment
Prepares the matrices for 'control_adjustment'	make_matrices
Prepares the matrices for 'control_adjustment'	make_matrices,data.frame-method make_matrices,ExpressionSet-method make_matrices,matrix-method make_matrices,RangedSummarizedExperiment-method make_matrices,SummarizedExperiment-method make_matrices-methods
Visualisation of the clustering	ttmap
Gives a list of associated genes per cluster	ttmap_sgn_genes ttmap_sgn_genes_inter ttmap_sgn_genes_inter2
Reading, writing and annotation files	mat2pcl read_pcl write_pcl