tricycle

DOI: 10.18129/B9.bioc.tricycle    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see tricycle.

tricycle: Transferable Representation and Inference of cell cycle

Bioconductor version: 3.15

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>

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")

 

HTML	R Script	tricycle: Transferable Representation and Inference of Cell Cycle
PDF		Reference Manual
Text		NEWS

Details

biocViews	BiologicalQuestion, DimensionReduction, ImmunoOncology, RNASeq, SingleCell, Software, Transcription, Transcriptomics
Version	1.4.0
In Bioconductor since	BioC 3.13 (R-4.1) (1.5 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
LinkingTo
Suggests	testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, CircStats, cowplot, htmltools, Seurat, org.Hs.eg.db, org.Mm.eg.db
SystemRequirements
Enhances
URL	https://github.com/hansenlab/tricycle
BugReports	https://github.com/hansenlab/tricycle/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	tricycle_1.4.0.tar.gz
Windows Binary	tricycle_1.4.0.zip
macOS Binary (x86_64)	tricycle_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/tricycle
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/tricycle
Package Short Url	https://bioconductor.org/packages/tricycle/
Package Downloads Report	Download Stats