Package: tricycle 1.15.0

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:

On BioConductor:tricycle-1.15.0(bioc 3.21)tricycle-1.14.0(bioc 3.20)

singlecellsoftwaretranscriptomicsrnaseqtranscriptionbiologicalquestiondimensionreductionimmunooncology

6.54 score 25 stars 46 scripts 524 downloads 9 exports 116 dependencies

Last updated 5 months agofrom:f801f57657. Checks:1 OK, 7 NOTE, 1 ERROR. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 19 2025
R-4.5-winNOTEMar 19 2025
R-4.5-macNOTEMar 19 2025
R-4.5-linuxNOTEMar 19 2025
R-4.4-winNOTEMar 19 2025
R-4.4-macNOTEMar 19 2025
R-4.4-linuxNOTEMar 19 2025
R-4.3-winNOTEMar 19 2025
R-4.3-macERRORMar 19 2025

Exports:circle_scale_legenddiagnose_totalumiestimate_cycle_positionestimate_Schwabe_stagefit_periodic_loessplot_ccposition_denplot_emb_circle_scaleproject_cycle_spacerun_pca_cc_genes

Dependencies:abindAnnotationDbiaskpassassortheadbeachmatbeeswarmBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularBiostringsbitbit64blobbootcachemCairocircularclicodetoolscolorspacecpp11crayoncurlDBIDelayedArraydplyrdqrngfansifarverfastmapFNNformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggbeeswarmggnewscaleggplot2ggrastrggrepelgluegridExtragtablehttrIRangesirlbaisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellmvtnormnlmeopensslpheatmappillarpkgconfigplogrpngR6raggRColorBrewerRcppRcppAnnoyRcppEigenRcppMLRcppProgressrlangRSpectraRSQLitersvdRtsneS4ArraysS4VectorsScaledMatrixscalesscaterscattermorescuttleSingleCellExperimentsitmosnowSparseArraystringiSummarizedExperimentsyssystemfontstextshapingtibbletidyselectUCSC.utilsutf8uwotvctrsviporviridisviridisLitewithrXVector

tricycle: Transferable Representation and Inference of Cell Cycle

Rendered fromtricycle.Rmdusingknitr::rmarkdownon Mar 19 2025.

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