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Bioconductor - TSCAN

TSCAN

This is the released version of TSCAN; for the devel version, see TSCAN.

Tools for Single-Cell Analysis

Bioconductor version: Release (3.21)

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 "4.5") 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")

Details biocViews GUI, GeneExpression, Software, Visualization Version 1.46.0 In Bioconductor since BioC 3.0 (R-3.1) (10.5 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 See More Suggests knitr, testthat, scuttle, scran, metapod, BiocParallel, BiocNeighbors, batchelor Linking To Enhances Depends On Me OSCA.advanced, OSCA.multisample 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.

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