Package: tricycle 1.13.0

Shijie Zheng

tricycle: tricycle: Transferable Representation and Inference of cell cycle

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.

Authors:Shijie Zheng [aut, cre]

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tricycle.pdf |tricycle.html✨
tricycle/json (API)
NEWS

# Install 'tricycle' in R:

install.packages('tricycle', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/hansenlab/tricycle/issues

Datasets:

RevelioGeneList - 5 stage cell cycle gene marker list from Revelio
neuroRef - Pre-learned reference projection matrix from the Neurosphere dataset
neurosphere_example - Example SingleCellExperiment dataset

On BioConductor:tricycle-1.13.0(bioc 3.20)tricycle-1.12.0(bioc 3.19)

bioconductor-package

9 exports 0.71 score 118 dependencies

Last updated 2 months agofrom:f3ce911d39

Exports:circle_scale_legend diagnose_totalumi estimate_cycle_position estimate_Schwabe_stage fit_periodic_loess plot_ccposition_den plot_emb_circle_scale project_cycle_space run_pca_cc_genes

Dependencies:abind AnnotationDbi askpass beachmat beeswarm BH Biobase BiocGenerics BiocNeighbors BiocParallel BiocSingular Biostrings bit bit64 blob boot cachem Cairo circular cli codetools colorspace cpp11 crayon curl DBI DelayedArray DelayedMatrixStats dplyr dqrng fansi farver fastmap FNN formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggbeeswarm ggnewscale ggplot2 ggrastr ggrepel glue gridExtra gtable httr IRanges irlba isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell mvtnorm nlme openssl pheatmap pillar pkgconfig plogr png R6 ragg RColorBrewer Rcpp RcppAnnoy RcppEigen RcppHNSW RcppML RcppProgress rlang RSpectra RSQLite rsvd Rtsne S4Arrays S4Vectors ScaledMatrix scales scater scattermore scuttle SingleCellExperiment sitmo snow SparseArray sparseMatrixStats SummarizedExperiment sys systemfonts textshaping tibble tidyselect UCSC.utils utf8 uwot vctrs vipor viridis viridisLite withr XVector zlibbioc

tricycle: Transferable Representation and Inference of Cell Cycle

Shijie C. Zheng

Rendered fromtricycle.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2022-02-09
Started: 2021-02-23

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Get the cyclic legend	circle_scale_legend
Diagnostic function for UMI based datasets	diagnose_totalumi
Assign cell cycle position	estimate_cycle_position
Assign cell cycle stages using Schwabe method	estimate_Schwabe_stage
Fit periodic loess line with circular predictor	fit_periodic_loess
Pre-learned reference projection matrix from the Neurosphere dataset	neuroRef
Example SingleCellExperiment dataset	neurosphere_example
Plot cell cycle position kernel density stratified by a factor	plot_ccposition_den
Plot embedding with cyclic cell cycle position	plot_emb_circle_scale
Project data into the cell cycle pattern space	project_cycle_space
5 stage cell cycle gene marker list from Revelio	RevelioGeneList
Run PCA on Gene Ontology cell cycle genes	run_pca_cc_genes