CellTrails
This is the development version of CellTrails; for the stable release version, see CellTrails.
Reconstruction, visualization and analysis of branching trajectories
Bioconductor version: Development (3.24)
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.
Author: Daniel Ellwanger [aut, cre, cph]
Maintainer: Daniel Ellwanger <dc.ellwanger.dev at gmail.com>
citation("CellTrails")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("CellTrails")
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("CellTrails")| CellTrails: Reconstruction, visualization, and analysis of branching trajectories from single-cell expression data | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Clustering, DataRepresentation, DifferentialExpression, DimensionReduction, GeneExpression, ImmunoOncology, Sequencing, SingleCell, Software, TimeCourse |
| Version | 1.31.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (8 years) |
| License | Artistic-2.0 |
| 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 |
| System Requirements | |
| URL |
See More
| Suggests | AnnotationDbi, destiny, RUnit, scater, scran, knitr, org.Mm.eg.db, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | CellTrails_1.31.0.tar.gz |
| Windows Binary (x86_64) | CellTrails_1.31.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | CellTrails_1.31.0.tgz |
| macOS Binary (sonoma-arm64) | CellTrails_1.31.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CellTrails |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CellTrails |
| Bioc Package Browser | https://code.bioconductor.org/browse/CellTrails/ |
| Package Short Url | https://bioconductor.org/packages/CellTrails/ |
| Package Downloads Report | Download Stats |