TSCAN
Tools for Single-Cell Analysis
Bioconductor version: 3.23 · Package version: 1.50.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("TSCAN")Details
| Maintainer | Zhicheng Ji <zji4@jhu.edu> |
| Author | Zhicheng Ji [aut, cre], Hongkai Ji [aut], Aaron Lun [ctb] |
| License | GPL(>=2) |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | GUI, GeneExpression, Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/TSCAN/ |
Citation
From within R, enter citation("TSCAN"):
Zhicheng Ji, Hongkai Ji. TSCAN: Tools for Single-Cell Analysis. doi:10.18129/B9.bioc.TSCAN, R package version 1.50.0, https://bioconductor.org/packages/TSCAN.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | TSCAN_1.50.0.tar.gz |
| Windows binary (x86_64) | TSCAN_1.50.0.zip |
| macOS binary (arm64) | TSCAN_1.50.0.tgz |
| macOS binary (x86_64) | TSCAN_1.50.0.tgz |
Dependencies
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
Suggests: knitr, testthat, scuttle, scran, metapod, BiocParallel, BiocNeighbors, batchelor