tricycle
tricycle: Transferable Representation and Inference of cell cycle
Bioconductor version: 3.23 · Package version: 1.20.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
The package contains functions to infer and visualize cell cycle process using Single Cell RNASeq data. It exploits the idea of transfer learning, projecting new data to the previous learned biologically interpretable space. We provide a pre-learned cell cycle space, which could be used to infer cell cycle time of human and mouse single cell samples. In addition, we also offer functions to visualize cell cycle time on different embeddings and functions to build new reference.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("tricycle")Details
| Maintainer | Shijie Zheng <shijieczheng@gmail.com> |
| Author | Shijie Zheng [aut, cre] |
| License | GPL-3 |
| URL | https://github.com/hansenlab/tricycle |
| Bug Reports | https://github.com/hansenlab/tricycle/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | BiologicalQuestion, DimensionReduction, ImmunoOncology, RNASeq, SingleCell, Software, Transcription, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/tricycle/ |
Citation
From within R, enter citation("tricycle"):
Shijie Zheng. tricycle: tricycle: Transferable Representation and Inference of cell cycle. doi:10.18129/B9.bioc.tricycle, R package version 1.20.0, https://bioconductor.org/packages/tricycle.
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 | tricycle_1.20.0.tar.gz |
| Windows binary (x86_64) | tricycle_1.20.0.zip |
| macOS binary (arm64) | tricycle_1.20.0.tgz |
| macOS binary (x86_64) | tricycle_1.20.0.tgz |
Dependencies
Depends: R (>= 4.0), SingleCellExperiment
Imports: methods, circular, ggplot2, ggnewscale, AnnotationDbi, scater, GenomicRanges, IRanges, S4Vectors, scattermore, dplyr, RColorBrewer, grDevices, stats, SummarizedExperiment, utils
Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, CircStats, cowplot, htmltools, Seurat, org.Hs.eg.db, org.Mm.eg.db