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:
tricycle_1.15.0.tar.gz
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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
- 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-1.15.0(bioc 3.21)tricycle-1.14.0(bioc 3.20)
singlecellsoftwaretranscriptomicsrnaseqtranscriptionbiologicalquestiondimensionreductionimmunooncology
Last updated 2 months agofrom:f801f57657. Checks:OK: 1 NOTE: 5 ERROR: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 19 2024 |
| R-4.5-win | NOTE | Dec 19 2024 |
| R-4.5-linux | NOTE | Dec 19 2024 |
| R-4.4-win | NOTE | Dec 19 2024 |
| R-4.4-mac | NOTE | Dec 19 2024 |
| R-4.3-win | NOTE | Dec 19 2024 |
| R-4.3-mac | ERROR | Dec 19 2024 |
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.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellmvtnormnlmeopensslpheatmappillarpkgconfigplogrpngR6raggRColorBrewerRcppRcppAnnoyRcppEigenRcppMLRcppProgressrlangRSpectraRSQLitersvdRtsneS4ArraysS4VectorsScaledMatrixscalesscaterscattermorescuttleSingleCellExperimentsitmosnowSparseArraySummarizedExperimentsyssystemfontstextshapingtibbletidyselectUCSC.utilsutf8uwotvctrsviporviridisviridisLitewithrXVectorzlibbioc
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 |
