Package: tricycle Type: Package Title: tricycle: Transferable Representation and Inference of cell cycle Version: 1.21.0 Authors@R: c( person("Shijie", "Zheng", role=c("aut", "cre"), email="shijieczheng@gmail.com")) Description: 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. 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 License: GPL-3 VignetteBuilder: knitr Encoding: UTF-8 LazyData: FALSE RoxygenNote: 7.1.2 biocViews: SingleCell, Software, Transcriptomics, RNASeq, Transcription, BiologicalQuestion, DimensionReduction, ImmunoOncology URL: https://github.com/hansenlab/tricycle BugReports: https://github.com/hansenlab/tricycle/issues Config/pak/sysreqs: libpng-dev libssl-dev zlib1g-dev Repository: https://bioc.r-universe.dev Date/Publication: 2026-04-28 12:55:43 UTC RemoteUrl: https://github.com/bioc/tricycle RemoteRef: HEAD RemoteSha: f0213737dd0865951fbf143cbf08f80d76094ac5 NeedsCompilation: no Packaged: 2026-07-04 04:29:56 UTC; root Author: Shijie Zheng [aut, cre] Maintainer: Shijie Zheng