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structure.","https://schema.org",{"og:url":83,"og:type":124,"og:title":65,"og:site_name":95,"og:description":67},"article",{"robots":126,"canonical":83},"index,follow",{"doc_id":128,"site_id":62},238838,1790485758,{"code":4,"msg":5,"data":131},{"doc_id":128,"user_id":132,"nickname":92,"user_avatar":133,"doc_module":4,"category_id":29,"category_name":30,"doc_title":65,"doc_description":67,"doc_content":134,"file_id":135,"file_url":136,"file_type":137,"file_size":138,"view_count":29,"is_deleted":4,"is_public":8,"is_downloadable":8,"audit_status":8,"page_count":139,"language":140,"language_code":63,"site_id":62,"html_lang":63,"table_of_contents":141,"faqs":142,"seo_title":143,"seo_description":67,"update_tm":144,"read_time":145},2336478503145,"https://ap-avatar.wpscdn.com/davatar_276721f389ce27ea32af1340a28f341c","Package ‘destiny’  \nMay 29, 2024  \nType Package  \nTitle Creates diffusion maps Version 3.18.0  \nDate 2014-12-19  \nDescription Create and plot diffusion maps.  \nLicense GPL-3  \nURL [https://theislab.github.io/destiny/](https://theislab.github.io/destiny/),  \n[https://github.com/theislab/destiny/](https://github.com/theislab/destiny/),  \n[https://www.helmholtz-muenchen.de/icb/destiny](https://www.helmholtz-muenchen.de/icb/destiny),  \n[https://bioconductor.org/packages/destiny](https://bioconductor.org/packages/destiny),  \n[https://doi.org/10.1093/bioinformatics/btv715](https://doi.org/10.1093/bioinformatics/btv715)[ ](https://doi.org/10.1093/bioinformatics/btv715)BugReports [https://github.com/theislab/destiny/issues](https://github.com/theislab/destiny/issues)[ ](https://github.com/theislab/destiny/issues)Encoding UTF-8  \nDepends R (>= 3.4.0)  \nImports methods, graphics, grDevices, grid, utils, stats, Matrix, Rcpp (>= 0.10.3), RcppEigen, RSpectra (>= 0.14-0), irlba, pcaMethods, Biobase, BiocGenerics, SummarizedExperiment, SingleCellExperiment, ggplot2, ggplot.multistats, rlang, tidyr, tidyselect, ggthemes, VIM, knn.covertree, proxy, RcppHNSW, smoother, scales, scatterplot3d  \nLinkingTo Rcpp, RcppEigen, grDevices SystemRequirements C++11 NeedsCompilation yes  \nEnhances rgl, SingleCellExperiment  \nSuggests knitr, rmarkdown, igraph, testthat, FNN, tidyverse, gridExtra, cowplot, conflicted, viridis, rgl, scRNAseq, [org.Mm.eg.db](org.Mm.eg.db), scran, repr  \nVignetteBuilder knitr  \n2 Contents  \nbiocViews CellBiology, CellBasedAssays, Clustering, Software,  \nVisualization  \nCollate 'RcppExports.R' 'aaa.r' 'accessor-generics.r' 'censoring.r''colorlegend.r' 'cube_helix.r' 'dataset-helpers.r'  \n'destiny-package.r' 's4-unions.r' 'dist-matrix-coerce.r'  \n'sigmas.r' 'diffusionmap.r' 'diffusionmap-methods-accession.r'  \n'diffusionmap-methods.r' 'plothelpers.r'  \n'diffusionmap-plotting.r' 'dpt-branching.r' 'dpt-helpers.r'  \n'dpt.r' 'dpt-methods-matrix.r' 'dpt-methods.r' 'utils.r'  \n'dpt-plotting.r' 'eig_decomp.r' 'expressionset-helpers.r'  \n'find_dm_k.r' 'gene-relevance.r' 'gene-relevance-methods.r'  \n'gene-relevance-plotting-differential-map.r'  \n'gene-relevance-plotting-gr-map.r'  \n'gene-relevance-plotting-rank.r' 'gene-relevance-plotting.r'  \n'guo-data.r' 'knn.r' 'l_which.r' 'methods-coercion.r'  \n'methods-extraction.r' 'methods-update.r' 'predict.r'  \n'projection-dist.r' 'rankcor.r' 'sigmas-plotting.r'RoxygenNote 7.2.3  \ngit_url [https://git.bioconductor.org/packages/destiny](https://git.bioconductor.org/packages/destiny)  \n[git_branch](git_branch RELEASE_3_19)[ RELEASE_3_19](git_branch RELEASE_3_19)[ ](git_branch RELEASE_3_19)[git_last_commit](git_last_commit 4cb2bd0)[ 4cb2bd0](git_last_commit 4cb2bd0)[ ](git_last_commit 4cb2bd0)git_last_commit_date 2024-04-30 Repository Bioconductor 3.19 Date/Publication 2024-05-29  \nAuthor Philipp Angerer [cre, aut](\u003C[https://orcid.org/0000-0002-0369-2888](https://orcid.org/0000-0002-0369-2888)>),  \nLaleh Haghverdi [ctb],  \nMaren Büttner [ctb](\u003C[https://orcid.org/0000-0002-6189-3792](https://orcid.org/0000-0002-6189-3792)>),  \nFabian Theis [ctb](\u003C[https://orcid.org/0000-0002-2419-1943](https://orcid.org/0000-0002-2419-1943)>),  \nCarsten Marr [ctb](\u003C[https://orcid.org/0000-0003-2154-4552](https://orcid.org/0000-0003-2154-4552)>),  \nFlorian Büttner [ctb](\u003C[https://orcid.org/0000-0001-5587-6761](https://orcid.org/0000-0001-5587-6761)>)  \nMaintainer Philipp Angerer \u003C[phil.angerer@gmail.com](phil.angerer@gmail.com)>  \nContents  \nCoercion methods ...................................... 3  \ncolorlegend ......................................... 4  \ncube_helix .......................................... 6  \ndestiny ............................................ 8  \ndestiny generics ....................................... 8  \nDiffusionMap accession methods .............................. 9  \nDiffusionMap methods ................................... 11  \nDiffusionMap-class ..................................... 12  \ndm","cbCaisurtoajYDew","https://ap.wps.com/l/cbCaisurtoajYDew","pdf",229838,46,"English","# Coercion methods\n# colorlegend\n# cube_helix\n# destiny\n## DiffusionMap accession methods\n## DiffusionMap methods\n## DiffusionMap-class\n## dm_predict\n## DPT matrix methods\n## DPT methods\n## DPT-class\n## eig_decomp\n## ExpressionSet helper methods\n## Extraction methods\n## find_dm_k\n## find_knn\n## find_sigmas\n## find_tips\n## Gene Relevance methods\n## GeneRelevance-class\n## guo\n## l_which\n## plot.DiffusionMap\n## plot.DPT\n## plot.Sigmas\n## plot_differential_map\n## projection_dist\n## random_root\n## Sigmas-class\n## updateObject methods\n# Index","[{\"question\":\"What does the destiny package provide?\",\"answer\":\"It provides functions to create and plot diffusion maps and to work with DPT objects. It includes related utilities for parameter selection, computations, and visualization.\"},{\"question\":\"How are diffusion map and DPT results represented?\",\"answer\":\"The package uses DiffusionMap and DPT objects as core representations. It also includes methods to convert these objects into other class formats such as data frames or matrices.\"},{\"question\":\"What main types of functionality are documented?\",\"answer\":\"The documentation spans coercion/conversion methods, diffusion map computation methods (including eigen decomposition and sigma selection), DPT methods (including branching), plotting helpers, and gene relevance methods for interpreting map structure.\"}]","destiny - Creates diffusion maps - package documentation | PDF",1789139917,116]