tricycle
This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see tricycle.
tricycle: Transferable Representation and Inference of cell cycle
Bioconductor version: 3.16
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.
Author: Shijie Zheng [aut, cre]
Maintainer: Shijie Zheng <shijieczheng at gmail.com>
citation("tricycle")):
Installation
To install this package, start R (version "4.2") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("tricycle")
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("tricycle")| tricycle: Transferable Representation and Inference of Cell Cycle | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BiologicalQuestion, DimensionReduction, ImmunoOncology, RNASeq, SingleCell, Software, Transcription, Transcriptomics |
| Version | 1.6.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (3 years) |
| License | GPL-3 |
| Depends | R (>= 4.0), SingleCellExperiment |
| Imports | methods, circular, ggplot2, ggnewscale, AnnotationDbi, scater, GenomicRanges, IRanges, S4Vectors, scattermore, dplyr, RColorBrewer, grDevices, stats, SummarizedExperiment, utils |
| System Requirements | |
| URL | https://github.com/hansenlab/tricycle |
| Bug Reports | https://github.com/hansenlab/tricycle/issues |
See More
| Suggests | testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, CircStats, cowplot, htmltools, Seurat, org.Hs.eg.db, org.Mm.eg.db |
| 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 | tricycle_1.6.0.tar.gz |
| Windows Binary | tricycle_1.6.0.zip |
| macOS Binary (x86_64) | tricycle_1.6.0.tgz |
| macOS Binary (arm64) | tricycle_1.6.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/tricycle |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/tricycle |
| Bioc Package Browser | https://code.bioconductor.org/browse/tricycle/ |
| Package Short Url | https://bioconductor.org/packages/tricycle/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.16 | Source Archive |