TSCAN

DOI: 10.18129/B9.bioc.TSCAN    

Tools for Single-Cell Analysis

Bioconductor version: Release (3.15)

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>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("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	1.34.0
In Bioconductor since	BioC 3.0 (R-3.1) (8 years)
License	GPL(>=2)
Depends	SingleCellExperiment, TrajectoryUtils
Imports	ggplot2, shiny, plyr, grid, fastICA, igraph, combinat, mgcv, mclust, gplots, methods, stats, Matrix, SummarizedExperiment, DelayedArray, S4Vectors
LinkingTo
Suggests	knitr, testthat, scuttle, scran, metapod, BiocParallel, BiocNeighbors, batchelor
SystemRequirements
Enhances
URL
Depends On Me	OSCA.advanced, OSCA.multisample
Imports Me	ctgGEM, FEAST, singleCellTK
Suggests Me	condiments
Links To Me
Build Report

Package Archives

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

Source Package	TSCAN_1.34.0.tar.gz
Windows Binary	TSCAN_1.34.0.zip
macOS Binary (x86_64)	TSCAN_1.34.0.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