CellTrails
Reconstruction, visualization and analysis of branching trajectories
Bioconductor version: 3.23 · Package version: 1.30.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
CellTrails is an unsupervised algorithm for the de novo chronological ordering, visualization and analysis of single-cell expression data. CellTrails makes use of a geometrically motivated concept of lower-dimensional manifold learning, which exhibits a multitude of virtues that counteract intrinsic noise of single cell data caused by drop-outs, technical variance, and redundancy of predictive variables. CellTrails enables the reconstruction of branching trajectories and provides an intuitive graphical representation of expression patterns along all branches simultaneously. It allows the user to define and infer the expression dynamics of individual and multiple pathways towards distinct phenotypes.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("CellTrails")Details
| Maintainer | Daniel Ellwanger <dc.ellwanger.dev@gmail.com> |
| Author | Daniel Ellwanger [aut, cre, cph] |
| License | Artistic-2.0 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Clustering, DataRepresentation, DifferentialExpression, DimensionReduction, GeneExpression, ImmunoOncology, Sequencing, SingleCell, Software, TimeCourse |
| Package Short Url | https://bioconductor.org/packages/CellTrails/ |
Citation
From within R, enter citation("CellTrails"):
Daniel Ellwanger. CellTrails: Reconstruction, visualization and analysis of branching trajectories. doi:10.18129/B9.bioc.CellTrails, R package version 1.30.0, https://bioconductor.org/packages/CellTrails.
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 | CellTrails_1.30.0.tar.gz |
| Windows binary (x86_64) | CellTrails_1.30.0.zip |
| macOS binary (arm64) | CellTrails_1.30.0.tgz |
| macOS binary (x86_64) | CellTrails_1.30.0.tgz |
Dependencies
Depends: R (>= 3.5), SingleCellExperiment
Imports: BiocGenerics, Biobase, cba, dendextend, dtw, EnvStats, ggplot2, ggrepel, grDevices, igraph, maptree, methods, mgcv, reshape2, Rtsne, stats, splines, SummarizedExperiment, utils
Suggests: AnnotationDbi, destiny, RUnit, scater, scran, knitr, org.Mm.eg.db, rmarkdown