1 Introduction | 2 Prepare the data | 3 TTMap part1: Adjustement of the control group (ctrl_adj) | 4 TTMap part1: Hyperrectangle deviation assessement (hda) | 5 TTMap part2: Global-to-local Mapper (gtlmap) | 6 TTMap: Finding the significant genes (sgn_genes) | 7 Conclusion
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:
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✨
DESCRIPTION
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.
softwaremicroarraydifferentialexpressionmultiplecomparisonclusteringclassification
Last updated from:d2b271c7bb. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 230 | ||
| linux-devel-x86_64 | NOTE | 395 | ||
| source / vignettes | OK | 290 | ||
| linux-release-x86_64 | NOTE | 378 | ||
| macos-release-arm64 | NOTE | 176 | ||
| macos-oldrel-arm64 | NOTE | 165 | ||
| windows-devel | NOTE | 216 | ||
| windows-release | NOTE | 231 | ||
| windows-oldrel | NOTE | 230 | ||
| wasm-release | OK | 162 |
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:abindbase64encBiobaseBiocGenericsbslibcachemclicolorRampsDelayedArraydigestevaluatefastmapfontawesomefsgenericsGenomicRangeshighrhtmltoolshtmlwidgetsIRangesjquerylibjsonliteknitrlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeR6rappdirsrglrlangrmarkdownS4ArraysS4VectorssassSeqinfoSparseArraySummarizedExperimenttinytexxfunXVectoryaml
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 |