TSCAN

Tools for Single-Cell Analysis

Bioconductor version: Release (3.20)

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 "4.4") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GUI, GeneExpression, Software, Visualization
Version	1.44.0
In Bioconductor since	BioC 3.0 (R-3.1) (10 years)
License	GPL(>=2)
Depends	R (>= 4.4.0), SingleCellExperiment, TrajectoryUtils
Imports	ggplot2, shiny, plyr, grid, fastICA, igraph, combinat, mgcv, mclust, gplots, methods, stats, Matrix, SummarizedExperiment, SparseArray(>= 1.5.23), DelayedArray(>= 0.31.9), S4Vectors
System Requirements
URL

Suggests	knitr, testthat, scuttle, scran, metapod, BiocParallel, BiocNeighbors, batchelor
Linking To
Enhances
Depends On Me
Imports Me	FEAST, singleCellTK, DIscBIO
Suggests Me	condiments
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	TSCAN_1.44.0.tar.gz
Windows Binary (x86_64)	TSCAN_1.44.0.zip
macOS Binary (x86_64)	TSCAN_1.44.0.tgz
macOS Binary (arm64)	TSCAN_1.44.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/TSCAN
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/TSCAN
Bioc Package Browser	https://code.bioconductor.org/browse/TSCAN/
Package Short Url	https://bioconductor.org/packages/TSCAN/
Package Downloads Report	Download Stats