Package: r-bioc-scran (1.32.0+dfsg-1 and others)

[ Source: r-bioc-scran  ]

BioConductor methods for single-cell RNA-Seq data analysis

Implements functions for low-level analyses of single-cell RNA-seq data. Methods are provided for normalization of cell-specific biases, assignment of cell cycle phase, detection of highly variable and significantly correlated genes, identification of marker genes, and other common tasks in routine single-cell analysis workflows.

Other Packages Related to r-bioc-scran

• dep: libblas3 [sparc64]

  Basic Linear Algebra Reference implementations, shared library

  or libblas.so.3

  virtual package provided by libatlas3-base, libblas3, libblis4-openmp, libblis4-pthread, libblis4-serial, libopenblas0-openmp, libopenblas0-pthread, libopenblas0-serial

• dep: libc6 (>= 2.27) [riscv64]

  GNU C Library: Shared libraries
  also a virtual package provided by libc6-udeb

  dep: libc6 (>= 2.29) [not alpha, ia64, riscv64, sh4]

  dep: libc6 (>= 2.37) [sh4]

• dep: libc6.1 (>= 2.29) [alpha]

  GNU C Library: Shared libraries
  also a virtual package provided by libc6.1-udeb

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

• dep: libgcc-s1 (>= 3.0) [not alpha, hppa, ia64, riscv64, sh4, sparc64]

  GCC support library

  dep: libgcc-s1 (>= 3.4) [alpha, riscv64, sh4, sparc64]

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

• dep: libgcc-s4 (>= 4.1.1) [hppa]

  GCC support library

• dep: libgfortran5 (>= 8) [sparc64]

  Runtime library for GNU Fortran applications

• dep: liblapack3

  Library of linear algebra routines 3 - shared version

  or liblapack.so.3

  virtual package provided by libatlas3-base, liblapack3, libopenblas0-openmp, libopenblas0-pthread, libopenblas0-serial

• dep: libstdc++6 (>= 11) [x32]

  GNU Standard C++ Library v3

  dep: libstdc++6 (>= 13.1) [hppa, ia64, sh4]

  dep: libstdc++6 (>= 14) [not hppa, ia64, sh4, x32]

• dep: libunwind8 [ia64]

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

• dep: r-api-4.0

  virtual package provided by r-base-core

• dep: r-api-bioc-3.16 [x32]

  Package not available

• dep: r-api-bioc-3.18 [hppa, ia64, sh4]

  Package not available

• dep: r-api-bioc-3.19 [not hppa, ia64, sh4, x32]

  virtual package provided by r-bioc-biocgenerics

• dep: r-base-core (>= 4.2.2.20221110-2) [x32]

  GNU R core of statistical computation and graphics system

• dep: r-bioc-beachmat [hppa, ia64, sh4, x32]

  I/O for several formats storing matrix data

  dep: r-bioc-beachmat (>= 2.20.0) [not hppa, ia64, sh4, x32]

• dep: r-bioc-biocgenerics [hppa, ia64, sh4, x32]

  generic functions for Bioconductor

  dep: r-bioc-biocgenerics (>= 0.50.0) [not hppa, ia64, sh4, x32]

• dep: r-bioc-biocparallel [hppa, ia64, sh4, x32]

  BioConductor facilities for parallel evaluation

  dep: r-bioc-biocparallel (>= 1.38.0) [not hppa, ia64, sh4, x32]

• dep: r-bioc-biocsingular [hppa, ia64, sh4, x32]

  Singular Value Decomposition for Bioconductor Packages

  dep: r-bioc-biocsingular (>= 1.20.0) [not hppa, ia64, sh4, x32]

• dep: r-bioc-bluster [hppa, ia64, sh4, x32]

  Clustering Algorithms for Bioconductor

  dep: r-bioc-bluster (>= 1.14.0) [not hppa, ia64, sh4, x32]

• dep: r-bioc-delayedarray [hppa, ia64, sh4, x32]

  BioConductor delayed operations on array-like objects

  dep: r-bioc-delayedarray (>= 0.30.1) [not hppa, ia64, sh4, x32]

• dep: r-bioc-delayedmatrixstats [hppa, ia64, sh4, x32]

  Functions on Rows and Columns of 'DelayedMatrix' Objects

  dep: r-bioc-delayedmatrixstats (>= 1.26.0) [not hppa, ia64, sh4, x32]

• dep: r-bioc-edger [hppa, ia64, sh4, x32]

  Empirical analysis of digital gene expression data in R

  dep: r-bioc-edger (>= 4.2.0) [not hppa, ia64, sh4, x32]

• dep: r-bioc-limma [hppa, ia64, sh4, x32]

  linear models for microarray data

  dep: r-bioc-limma (>= 3.60.3) [not hppa, ia64, sh4, x32]

• dep: r-bioc-metapod [hppa, ia64, sh4, x32]

  GNU R meta-analyses on P-Values of differential analyses

  dep: r-bioc-metapod (>= 1.12.0) [not hppa, ia64, sh4, x32]

• dep: r-bioc-s4vectors [hppa, ia64, sh4, x32]

  BioConductor S4 implementation of vectors and lists

  dep: r-bioc-s4vectors (>= 0.42.1) [not hppa, ia64, sh4, x32]

• dep: r-bioc-scuttle [hppa, ia64, sh4, x32]

  BioConductor single-cell RNA-Seq analysis utilities

  dep: r-bioc-scuttle (>= 1.14.0) [not hppa, ia64, sh4, x32]

• dep: r-bioc-singlecellexperiment [hppa, ia64, sh4, x32]

  S4 Classes for Single Cell Data

  dep: r-bioc-singlecellexperiment (>= 1.26.0) [not hppa, ia64, sh4, x32]

• dep: r-bioc-summarizedexperiment [hppa, ia64, sh4, x32]

  BioConductor assay container

  dep: r-bioc-summarizedexperiment (>= 1.34.0) [not hppa, ia64, sh4, x32]

• dep: r-cran-bh

  (Virtual) GNU R package to provide BH

• dep: r-cran-dqrng

  GNU R fast pseudo random number generators

• dep: r-cran-igraph

  GNU R network analysis and visualization

• dep: r-cran-matrix

  GNU R package of classes for dense and sparse matrices

• dep: r-cran-rcpp

  GNU R package for Seamless R and C++ Integration

• dep: r-cran-statmod

  GNU R package providing algorithms and functions for statistical modeling

• sug: r-bioc-biobase [hppa, ia64, sh4, x32]

  base functions for Bioconductor

• sug: r-bioc-biocstyle

  standard styles for vignettes and other Bioconductor documents

• sug: r-bioc-deseq2

  R package for RNA-Seq Differential Expression Analysis

• sug: r-bioc-hdf5array

  HDF5 backend for DelayedArray objects

• sug: r-bioc-monocle [hppa, ia64, sh4, x32]

  clustering, differential expression, and trajectory analysis for RNA-Seq

• sug: r-bioc-residualmatrix

  Creating a DelayedMatrix of Regression Residuals

• sug: r-bioc-scaledmatrix

  creating a DelayedMatrix of scaled and centered values using GNU R

• sug: r-bioc-scater

  Single-Cell Analysis Toolkit for Gene Expression Data in R

• sug: r-bioc-scrnaseq

  Collection of Public Single-Cell RNA-Seq Datasets

• sug: r-cran-dynamictreecut

  Methods for Detection of Clusters in Hierarchical Clustering

• sug: r-cran-knitr

  GNU R package for dynamic report generation using Literate Programming

• sug: r-cran-pheatmap

  GNU R package to create pretty heatmaps

• sug: r-cran-rmarkdown

  convert R markdown documents into a variety of formats

• sug: r-cran-testthat

  GNU R testsuite

Download r-bioc-scran

Download for all available architectures

Architecture	Version	Package Size	Installed Size	Files
alpha (unofficial port)	1.32.0+dfsg-1	982.9 kB	1,492.0 kB	[list of files]
amd64	1.32.0+dfsg-1	994.0 kB	1,409.0 kB	[list of files]
arm64	1.32.0+dfsg-1	976.7 kB	1,429.0 kB	[list of files]
hppa (unofficial port)	1.30.2+dfsg-1	968.1 kB	1,429.0 kB	[list of files]
ia64 (unofficial port)	1.30.2+dfsg-1	985.8 kB	1,683.0 kB	[list of files]
mips64el	1.32.0+dfsg-1	975.2 kB	1,533.0 kB	[list of files]
ppc64 (unofficial port)	1.32.0+dfsg-1	990.9 kB	1,561.0 kB	[list of files]
ppc64el	1.32.0+dfsg-1	989.5 kB	1,493.0 kB	[list of files]
riscv64	1.32.0+dfsg-1	990.3 kB	1,336.0 kB	[list of files]
s390x	1.32.0+dfsg-1	995.2 kB	1,436.0 kB	[list of files]
sh4 (unofficial port)	1.30.2+dfsg-1	987.2 kB	1,410.0 kB	[list of files]
sparc64 (unofficial port)	1.32.0+dfsg-1	969.0 kB	2,076.0 kB	[list of files]
x32 (unofficial port)	1.26.2+dfsg-1	964.7 kB	1,342.0 kB	[list of files]