套件：r-bioc-densvis（1.10.3+dfsg-1） [debports]
density-preserving data visualization via non-linear dimensionality reduction
Implements the density-preserving modification to t-SNE and UMAP described by Narayan et al. (2020) <doi:10.1101/2020.05.12.077776>. The non-linear dimensionality reduction techniques t-SNE and UMAP enable users to summarise complex high-dimensional sequencing data such as single cell RNAseq using lower dimensional representations. These lower dimensional representations enable the visualisation of discrete transcriptional states, as well as continuous trajectory (for example, in early development). However, these methods focus on the local neighbourhood structure of the data. In some cases, this results in misleading visualisations, where the density of cells in the low-dimensional embedding does not represent the transcriptional heterogeneity of data in the original high-dimensional space. den-SNE and densMAP aim to enable more accurate visual interpretation of high-dimensional datasets by producing lower-dimensional embeddings that accurately represent the heterogeneity of the original high-dimensional space, enabling the identification of homogeneous and heterogeneous cell states. This accuracy is accomplished by including in the optimisation process a term which considers the local density of points in the original high-dimensional space. This can help to create visualisations that are more representative of heterogeneity in the original high-dimensional space.
其他與 r-bioc-densvis 有關的套件
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- dep: libc6 (>= 2.29)
- GNU C 函式庫：共用函式庫
同時作為一個虛擬套件由這些套件填實： libc6-udeb
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- dep: libgcc-s1 (>= 3.0)
- GCC 支援函式庫
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- dep: libgomp1 (>= 6)
- GCC OpenMP (GOMP) support library
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- dep: libstdc++6 (>= 13.1)
- GNU Standard C++ Library v3
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- dep: r-api-4.0
- 本虛擬套件由這些套件填實： r-base-core
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- dep: r-api-bioc-3.17
- 套件暫時不可用
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- dep: r-bioc-basilisk
- freezing Python dependencies inside Bioconductor packages
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- dep: r-cran-assertthat
- GNU R easy pre and post assertions
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- dep: r-cran-irlba
- GNU R fast truncated SVD, PCA and symmetric eigendecomposition
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- dep: r-cran-rcpp
- GNU R package for Seamless R and C++ Integration
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- dep: r-cran-reticulate
- R interface to Python modules, classes, and functions
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- sug: r-bioc-biocstyle
- standard styles for vignettes and other Bioconductor documents
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- sug: r-cran-ggplot2
- implementation of the Grammar of Graphics
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- sug: r-cran-knitr
- GNU R package for dynamic report generation using Literate Programming
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- sug: r-cran-rmarkdown
- convert R markdown documents into a variety of formats
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- sug: r-cran-rtsne
- GNU R T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut
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- sug: r-cran-testthat
- GNU R testsuite
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- sug: r-cran-uwot
- GNU R uniform manifold approximation and projection (UMAP)