Paket: r-bioc-densvis (1.14.1+dfsg-1 och andra)

[ Källkod: r-bioc-densvis  ]

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.

Andra paket besläktade med r-bioc-densvis

• dep: libblas3 [sparc64]

  Basic Linear Algebra Reference implementations, shared library

  eller libblas.so.3

  virtuellt paket som tillhandahålls av libatlas3-base, libblas3, libblis4-openmp, libblis4-pthread, libblis4-serial, libopenblas0-openmp, libopenblas0-pthread, libopenblas0-serial

• dep: libc6 (>= 2.29) [ej alpha, ia64, sh4]

  GNU C-bibliotek: Delade bibliotek
  också ett virtuellt paket som tillhandahålls av libc6-udeb

  dep: libc6 (>= 2.37) [sh4]

• dep: libc6.1 (>= 2.29) [alpha]

  GNU C-bibliotek: Delade bibliotek
  också ett virtuellt paket som tillhandahålls av libc6.1-udeb

  dep: libc6.1 (>= 2.37) [ia64]

• dep: libgcc-s1 (>= 3.0) [amd64, arm64, ppc64, x32]

  GCC stödbibliotek

  dep: libgcc-s1 (>= 3.4) [alpha, sh4, sparc64]

  dep: libgcc-s1 (>= 4.2) [ia64]

• dep: libgcc-s2 (>= 4.2.1) [m68k]

  GCC stödbibliotek

• dep: libgcc-s4 (>= 4.1.1) [hppa]

  GCC stödbibliotek

• dep: libgfortran5 (>= 8) [sparc64]

  Runtime library for GNU Fortran applications

• dep: libgomp1 (>= 4.2.1) [amd64, arm64]

  GCC OpenMP (GOMP) support library

  dep: libgomp1 (>= 6) [ej amd64, arm64]

• dep: liblapack3 [sparc64]

  Library of linear algebra routines 3 - shared version

  eller liblapack.so.3

  virtuellt paket som tillhandahålls av libatlas3-base, liblapack3, libopenblas0-openmp, libopenblas0-pthread, libopenblas0-serial

• dep: libstdc++6 (>= 13.1) [ej amd64, arm64]

  GNU standardbibliotek v3 för C++

  dep: libstdc++6 (>= 14) [amd64, arm64]

• dep: libunwind8 [ia64]

  library to determine the call-chain of a program - runtime

• dep: r-api-4.0

  virtuellt paket som tillhandahålls av r-base-core

• dep: r-api-bioc-3.17 [ej amd64, arm64]

  Paketet inte tillgängligt

• dep: r-api-bioc-3.19 [amd64, arm64]

  virtuellt paket som tillhandahålls av r-bioc-biocgenerics

• dep: r-bioc-basilisk

  freezing Python dependencies inside Bioconductor packages

• dep: r-cran-assertthat

  GNU R easy pre and post assertions

• dep: r-cran-irlba

  GNU R fast truncated SVD, PCA and symmetric eigendecomposition

• dep: r-cran-rcpp

  GNU R package for Seamless R and C++ Integration

• dep: r-cran-reticulate

  R interface to Python modules, classes, and functions

• dep: r-cran-rtsne [amd64, arm64]

  GNU R T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut

• sug: r-bioc-biocstyle

  standard styles for vignettes and other Bioconductor documents

• sug: r-cran-ggplot2

  implementation of the Grammar of Graphics

• sug: r-cran-knitr

  GNU R package for dynamic report generation using Literate Programming

• sug: r-cran-rmarkdown

  convert R markdown documents into a variety of formats

• sug: r-cran-rtsne [ej amd64, arm64]

  GNU R T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut

• sug: r-cran-testthat

  GNU R testsuite

• sug: r-cran-uwot

  GNU R uniform manifold approximation and projection (UMAP)

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Hämtningar för alla tillgängliga arkitekturer

Arkitektur	Version	Paketstorlek	Installerad storlek	Filer
alpha (inofficiell anpassning)	1.10.3+dfsg-1	79,3 kbyte	214,0 kbyte	[filförteckning]
amd64	1.14.1+dfsg-1	82,6 kbyte	204,0 kbyte	[filförteckning]
arm64	1.14.1+dfsg-1	77,0 kbyte	216,0 kbyte	[filförteckning]
hppa (inofficiell anpassning)	1.10.3+dfsg-1	81,8 kbyte	212,0 kbyte	[filförteckning]
ia64 (inofficiell anpassning)	1.10.3+dfsg-1	92,0 kbyte	305,0 kbyte	[filförteckning]
m68k (inofficiell anpassning)	1.10.3+dfsg-1	77,7 kbyte	189,0 kbyte	[filförteckning]
ppc64 (inofficiell anpassning)	1.10.3+dfsg-1	86,1 kbyte	281,0 kbyte	[filförteckning]
sh4 (inofficiell anpassning)	1.10.3+dfsg-1	87,3 kbyte	213,0 kbyte	[filförteckning]
sparc64 (inofficiell anpassning)	1.10.3+dfsg-1	74,3 kbyte	1.115,0 kbyte	[filförteckning]
x32 (inofficiell anpassning)	1.10.3+dfsg-1	80,8 kbyte	193,0 kbyte	[filförteckning]