Tools for Single-Cell Analysis

Bioconductor version: Release (3.19)

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")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


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


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

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


biocViews GUI, GeneExpression, Software, Visualization
Version 1.42.0
In Bioconductor since BioC 3.0 (R-3.1) (9.5 years)
License GPL(>=2)
Depends SingleCellExperiment, TrajectoryUtils
Imports ggplot2, shiny, plyr, grid, fastICA, igraph, combinat, mgcv, mclust, gplots, methods, stats, Matrix, SummarizedExperiment, DelayedArray, S4Vectors
System Requirements
See More
Suggests knitr, testthat, scuttle, scran, metapod, BiocParallel, BiocNeighbors, batchelor
Linking To
Depends On Me OSCA.multisample
Imports Me FEAST, singleCellTK
Suggests Me condiments
Links To Me
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Package Archives

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

Source Package TSCAN_1.42.0.tar.gz
Windows Binary TSCAN_1.42.0.zip (64-bit only)
macOS Binary (x86_64) TSCAN_1.42.0.tgz
macOS Binary (arm64) TSCAN_1.42.0.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/
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