Package: SCORPIUS 1.0.9
SCORPIUS: Inferring Developmental Chronologies from Single-Cell RNA Sequencing Data
An accurate and easy tool for performing linear trajectory inference on single cells using single-cell RNA sequencing data. In addition, 'SCORPIUS' provides functions for discovering the most important genes with respect to the reconstructed trajectory, as well as nice visualisation tools. Cannoodt et al. (2016) <doi:10.1101/079509>.
Authors:
SCORPIUS_1.0.9.tar.gz
SCORPIUS_1.0.9.zip(r-4.5)SCORPIUS_1.0.9.zip(r-4.4)SCORPIUS_1.0.9.zip(r-4.3)
SCORPIUS_1.0.9.tgz(r-4.4-any)SCORPIUS_1.0.9.tgz(r-4.3-any)
SCORPIUS_1.0.9.tar.gz(r-4.5-noble)SCORPIUS_1.0.9.tar.gz(r-4.4-noble)
SCORPIUS_1.0.9.tgz(r-4.4-emscripten)SCORPIUS_1.0.9.tgz(r-4.3-emscripten)
SCORPIUS.pdf |SCORPIUS.html✨
SCORPIUS/json (API)
NEWS
| # Install 'SCORPIUS' in R: |
| install.packages('SCORPIUS', repos = c('https://rcannood.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/rcannood/scorpius/issues
- ginhoux - ScRNA-seq data of dendritic cell progenitors.
Last updated 1 years agofrom:a0a979076f. Checks:OK: 3 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 13 2024 |
| R-4.5-win | NOTE | Sep 13 2024 |
| R-4.5-linux | NOTE | Sep 13 2024 |
| R-4.4-win | NOTE | Sep 13 2024 |
| R-4.4-mac | NOTE | Sep 13 2024 |
| R-4.3-win | OK | Sep 13 2024 |
| R-4.3-mac | OK | Sep 13 2024 |
Exports:apply_minmax_scaleapply_quantile_scaleapply_uniform_scaledraw_trajectory_heatmapdraw_trajectory_plotextract_modulesgene_importancesgenerate_datasetinfer_trajectoryreduce_dimensionalityreverse_trajectoryscale_minmaxscale_quantilescale_uniformti_scorpius
Dependencies:assertthatbabelwhalebitbit64carrierclicliprcodetoolscolorspacecpp11crayondescdigestdplyrdynparamdynutilsdynwrapfansifarverforeachfsgenericsggplot2gluegtablehmsigraphirlbaisobanditeratorslabelinglatticelifecyclelmdslobstrmagrittrMASSMatrixmclustmgcvmunsellnlmepbapplypheatmappillarpkgconfigplyrprettyunitsprincurveprocessxprogressproxyCpspurrrR6rangerRANNRColorBrewerRcppRcppArmadilloRcppEigenreadrremotesreshape2rlangscalesstringistringrtibbletidyrtidyselectTSPtzdbutf8vctrsviridisLitevroomwithryaml
Investigating dendritic cell maturation in dendritic cell progenitors
Rendered fromginhoux.Rmdusingknitr::rmarkdownon Sep 13 2024.Last update: 2019-04-17
Started: 2016-01-12
Running SCORPIUS on an AnnData object
Rendered fromanndata.Rmdusingknitr::rmarkdownon Sep 13 2024.Last update: 2023-07-20
Started: 2023-01-27
Running SCORPIUS on a SingleCellExperiment object
Rendered fromsinglecellexperiment.Rmdusingknitr::rmarkdownon Sep 13 2024.Last update: 2023-07-19
Started: 2023-07-19
Trajectory inference from simulated data
Rendered fromsimulated-data.Rmdusingknitr::rmarkdownon Sep 13 2024.Last update: 2019-04-17
Started: 2016-01-12
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| SCORPIUS: Trajectory inference from single-cell RNA sequencing data. | SCORPIUS-package SCORPIUS |
| Draw time-series heatmap | draw_trajectory_heatmap |
| Visualise SCORPIUS | draw_trajectory_plot |
| Extract modules of features | extract_modules |
| Calculate the importance of a feature | gene_importances |
| Generate a synthetic dataset | generate_dataset |
| scRNA-seq data of dendritic cell progenitors. | ginhoux |
| Infer an initial trajectory through space | infer_initial_trajectory |
| Infer linear trajectory through space | infer_trajectory |
| Dimensionality reduction | reduce_dimensionality |
| Reverse a trajectory | reverse_trajectory |
| Infer a trajectory using SCORPIUS | ti_scorpius |
