Package: TTMap 1.29.0
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:
TTMap_1.29.0.tar.gz
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TTMap.pdf |TTMap.html✨
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-1.29.0(bioc 3.21)TTMap-1.28.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
softwaremicroarraydifferentialexpressionmultiplecomparisonclusteringclassification
Last updated 5 months agofrom:f7d844be1d. Checks:6 OK, 3 NOTE. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Mar 20 2025 |
| R-4.5-win | NOTE | Mar 20 2025 |
| R-4.5-mac | NOTE | Mar 20 2025 |
| R-4.5-linux | NOTE | Mar 20 2025 |
| R-4.4-win | OK | Mar 20 2025 |
| R-4.4-mac | OK | Mar 20 2025 |
| R-4.4-linux | OK | Mar 20 2025 |
| R-4.3-win | OK | Mar 20 2025 |
| R-4.3-mac | OK | Mar 20 2025 |
Exports:calcul_ecalcul_e_singlecontrol_adjustmentgenerate_correlationgenerate_euclideangenerate_mismatch_distancegenerate_p_val_correlationgenerate_single_cell_complete_mismatchgenerate_single_cell_mismatch_with_parameterhyperrectangle_deviation_assessmentmake_matricesread_pclttmapttmap_sgn_geneswrite_pcl
Dependencies:abindaskpassbase64encBiobaseBiocGenericsbslibcachemclicolorRampscrayoncurlDelayedArraydigestevaluatefastmapfontawesomefsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehighrhtmltoolshtmlwidgetshttrIRangesjquerylibjsonliteknitrlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslR6rappdirsrglrlangrmarkdownS4ArraysS4VectorssassSparseArraySummarizedExperimentsystinytexUCSC.utilsxfunXVectoryaml
Citation
To cite package ‘TTMap’ in publications use:
Jeitziner R (2017). TTMap: Two-Tier Mapper: a clustering tool based on topological data analysis. R package version 1.29.0, https://bioconductor.org/packages/TTMap.
ATTENTION: This citation information has been auto-generated from the package DESCRIPTION file and may need manual editing, see ‘help("citation")’.
Corresponding BibTeX entry:
@Manual{,
title = {TTMap: Two-Tier Mapper: a clustering tool based on
topological data analysis},
author = {Rachel Jeitziner},
year = {2017},
note = {R package version 1.29.0},
url = {https://bioconductor.org/packages/TTMap},
}
Readme and manuals
TTMap
R Software Package
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 |