Package: TSCAN 1.45.0
Zhicheng Ji
TSCAN: Tools for Single-Cell Analysis
Provides methods to perform trajectory analysis based on a minimum spanning tree constructed from cluster centroids. Computes pseudotemporal cell orderings by mapping cells in each cluster (or new cells) to the closest edge in the tree. Uses linear modelling to identify differentially expressed genes along each path through the tree. Several plotting and interactive visualization functions are also implemented.
Authors:
TSCAN_1.45.0.tar.gz
TSCAN_1.45.0.zip(r-4.5)TSCAN_1.45.0.zip(r-4.4)TSCAN_1.43.2.zip(r-4.3)
TSCAN_1.45.0.tgz(r-4.4-any)TSCAN_1.43.2.tgz(r-4.3-any)
TSCAN_1.45.0.tar.gz(r-4.5-noble)TSCAN_1.45.0.tar.gz(r-4.4-noble)
TSCAN_1.45.0.tgz(r-4.4-emscripten)TSCAN_1.43.2.tgz(r-4.3-emscripten)
TSCAN.pdf |TSCAN.html✨
TSCAN/json (API)
NEWS
| # Install 'TSCAN' in R: |
| install.packages('TSCAN', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- lpsdata - Sinlge-cell RNA-seq data for BMDC cells before and after LPS stimulation
On BioConductor:TSCAN-1.45.0(bioc 3.21)TSCAN-1.44.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
geneexpressionvisualizationgui
Last updated 2 months agofrom:a82164abf9. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 27 2024 |
| R-4.5-win | NOTE | Nov 27 2024 |
| R-4.5-linux | NOTE | Nov 27 2024 |
| R-4.4-win | NOTE | Nov 27 2024 |
| R-4.4-mac | NOTE | Nov 27 2024 |
| R-4.3-win | NOTE | Sep 14 2024 |
| R-4.3-mac | NOTE | Sep 14 2024 |
Exports:createClusterMSTdifftestexprmclustmapCellsToEdgesorderCellsorderscoreperCellEntropyplotmclustpreprocessquickPseudotimereportEdgesrowmeansinglegeneplottestPseudotimeTSCANorderTSCANui
Dependencies:abindaskpassbase64encBiobaseBiocGenericsbitopsbslibcachemcaToolsclicolorspacecombinatcommonmarkcpp11crayoncurlDelayedArraydigestfansifarverfastICAfastmapfontawesomefsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegplotsgtablegtoolshtmltoolshttpuvhttrigraphIRangesisobandjquerylibjsonliteKernSmoothlabelinglaterlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplyrpromisesR6rappdirsRColorBrewerRcpprlangS4ArraysS4VectorssassscalesshinySingleCellExperimentsourcetoolsSparseArraySummarizedExperimentsystibbleTrajectoryUtilsUCSC.utilsutf8vctrsviridisLitewithrxtableXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| difftest | difftest |
| exprmclust | exprmclust |
| Sinlge-cell RNA-seq data for BMDC cells before and after LPS stimulation | lpsdata |
| Map cells to edges | mapCellsToEdges mapCellsToEdges,ANY-method mapCellsToEdges,SingleCellExperiment-method mapCellsToEdges,SummarizedExperiment-method |
| Compute pseudotimes from the MST | orderCells |
| orderscore | orderscore |
| Compute the per-cell entropy | perCellEntropy perCellEntropy,ANY-method perCellEntropy,SummarizedExperiment-method |
| plotmclust | plotmclust |
| preprocess | preprocess |
| Quick MST-based pseudotime | quickPseudotime quickPseudotime,ANY-method quickPseudotime,SingleCellExperiment-method quickPseudotime,SummarizedExperiment-method |
| Report MST edge coordinates | reportEdges reportEdges,ANY-method reportEdges,SingleCellExperiment-method reportEdges,SummarizedExperiment-method |
| singlegeneplot | singlegeneplot |
| Test for differences along pseudotime | testPseudotime testPseudotime,ANY-method testPseudotime,SummarizedExperiment-method |
| TSCAN: Tools for Single-Cell ANalysis | TSCAN-package TSCAN |
| TSCANorder | TSCANorder |
| TSCANui | TSCANui |