tricycle

DOI: 10.18129/B9.bioc.tricycle    

This is the development version of tricycle; for the stable release version, see tricycle.

tricycle: Transferable Representation and Inference of cell cycle

Bioconductor version: Development (3.14)

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 (from within R, enter citation("tricycle")):

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.1.1
In Bioconductor since BioC 3.13 (R-4.1) (< 6 months)
License GPL-3
Depends R (>= 4.0), SingleCellExperiment
Imports methods, circular, ggplot2, 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_1.1.1.tar.gz
Windows Binary tricycle_1.1.1.zip
macOS 10.13 (High Sierra) tricycle_1.1.1.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

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