TSCAN
This is the development version of TSCAN; for the stable release version, see TSCAN.
Tools for Single-Cell Analysis
Bioconductor version: Development (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("TSCAN")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GUI, GeneExpression, Software, Visualization |
| Version | 1.45.0 |
| 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 |
See More
| 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_1.45.0.tar.gz |
| Windows Binary (x86_64) | TSCAN_1.45.0.zip (64-bit only) |
| macOS Binary (x86_64) | TSCAN_1.45.0.tgz |
| macOS Binary (arm64) | |
| 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 |