DOI: 10.18129/B9.bioc.TSCAN  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see TSCAN.

Tools for Single-Cell Analysis

Bioconductor version: 3.16

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")):


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


biocViews GUI, GeneExpression, Software, Visualization
Version 1.36.0
In Bioconductor since BioC 3.0 (R-3.1) (8.5 years)
License GPL(>=2)
Depends SingleCellExperiment, TrajectoryUtils
Imports ggplot2, shiny, plyr, grid, fastICA, igraph, combinat, mgcv, mclust, gplots, methods, stats, Matrix, SummarizedExperiment, DelayedArray, S4Vectors
Suggests knitr, testthat, scuttle, scran, metapod, BiocParallel, BiocNeighbors, batchelor
Depends On Me OSCA.advanced, OSCA.multisample
Imports Me ctgGEM, FEAST, singleCellTK
Suggests Me condiments
Links To Me
Build Report  

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Source Package TSCAN_1.36.0.tar.gz
Windows Binary TSCAN_1.36.0.zip
macOS Binary (x86_64) TSCAN_1.36.0.tgz
macOS Binary (arm64) TSCAN_1.36.0.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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