TSCAN

DOI: 10.18129/B9.bioc.TSCAN    

Tools for Single-Cell Analysis

Bioconductor version: Release (3.12)

Provides methods to perform trajectory analysis based on a minimum spanning tree constructed from cluster centroids. Computes pseudotemporal cell orderings by mapping cells in each cluster (or new cells) to the closest edge in the tree. Uses linear modelling to identify differentially expressed genes along each path through the tree. Several plotting and interactive visualization functions are also implemented.

Author: Zhicheng Ji [aut, cre], Hongkai Ji [aut], Aaron Lun [ctb]

Maintainer: Zhicheng Ji <zji4 at jhu.edu>

Citation (from within R, enter citation("TSCAN")):

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("TSCAN")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("TSCAN")

 

PDF R Script TSCAN: Tools for Single-Cell ANalysis
PDF   Reference Manual
Text   NEWS

Details

biocViews GUI, GeneExpression, Software, Visualization
Version 1.28.0
In Bioconductor since BioC 3.0 (R-3.1) (6 years)
License GPL(>=2)
Depends
Imports ggplot2, shiny, plyr, grid, fastICA, igraph, combinat, mgcv, mclust, gplots, methods, stats, Matrix, SummarizedExperiment, SingleCellExperiment, DelayedArray, S4Vectors
LinkingTo
Suggests knitr, testthat, beachmat, scuttle, scran, BiocParallel, BiocNeighbors, batchelor
SystemRequirements
Enhances
URL
Depends On Me
Imports Me ctgGEM
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package TSCAN_1.28.0.tar.gz
Windows Binary TSCAN_1.28.0.zip
macOS 10.13 (High Sierra) TSCAN_1.28.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/TSCAN
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/TSCAN
Package Short Url https://bioconductor.org/packages/TSCAN/
Package Downloads Report Download Stats

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