Pakket: r-bioc-densvis (1.14.1+dfsg-1 en anderen)

[ Bron: 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.

Andere aan r-bioc-densvis gerelateerde pakketten

• dep: libblas3 [sparc64]

  Basic Linear Algebra Reference implementations, shared library

  of libblas.so.3

  virtueel pakket geboden door libatlas3-base, libblas3, libblis4-openmp, libblis4-pthread, libblis4-serial, libopenblas0-openmp, libopenblas0-pthread, libopenblas0-serial

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

  GNU C Bibliotheek: Gedeelde bibliotheken
  Ook een virtueel pakket geboden door: libc6-udeb

  dep: libc6 (>= 2.37) [sh4]

• dep: libc6.1 (>= 2.29) [alpha]

  GNU C Bibliotheek: Gedeelde bibliotheken
  Ook een virtueel pakket geboden door: libc6.1-udeb

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

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

  GCC support bibliotheek

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

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

• dep: libgcc-s2 (>= 4.2.1) [m68k]

  GCC support bibliotheek

• dep: libgcc-s4 (>= 4.1.1) [hppa]

  GCC support bibliotheek

• 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) [niet amd64, arm64]

• dep: liblapack3 [sparc64]

  Library of linear algebra routines 3 - shared version

  of liblapack.so.3

  virtueel pakket geboden door libatlas3-base, liblapack3, libopenblas0-openmp, libopenblas0-pthread, libopenblas0-serial

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

  GNU Standard C++ Library v3

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

• dep: libunwind8 [ia64]

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

• dep: r-api-4.0

  virtueel pakket geboden door r-base-core

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

  Pakket niet beschikbaar

• dep: r-api-bioc-3.19 [amd64, arm64]

  virtueel pakket geboden door 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 [niet 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)

r-bioc-densvis downloaden

Pakket downloaden voor alle beschikbare platforms

Platform	Versie	Pakketgrootte	Geïnstalleerde grootte	Bestanden
alpha (unofficial port)	1.10.3+dfsg-1	79,3 kB	214,0 kB	[overzicht]
amd64	1.14.1+dfsg-1	82,6 kB	204,0 kB	[overzicht]
arm64	1.14.1+dfsg-1	77,0 kB	216,0 kB	[overzicht]
hppa (unofficial port)	1.10.3+dfsg-1	81,8 kB	212,0 kB	[overzicht]
ia64 (unofficial port)	1.10.3+dfsg-1	92,0 kB	305,0 kB	[overzicht]
m68k (unofficial port)	1.10.3+dfsg-1	77,7 kB	189,0 kB	[overzicht]
ppc64 (unofficial port)	1.10.3+dfsg-1	86,1 kB	281,0 kB	[overzicht]
sh4 (unofficial port)	1.10.3+dfsg-1	87,3 kB	213,0 kB	[overzicht]
sparc64 (unofficial port)	1.10.3+dfsg-1	74,3 kB	1.115,0 kB	[overzicht]
x32 (unofficial port)	1.10.3+dfsg-1	80,8 kB	193,0 kB	[overzicht]