Package: sccore 1.0.5
sccore: Core Utilities for Single-Cell RNA-Seq
Core utilities for single-cell RNA-seq data analysis. Contained within are utility functions for working with differential expression (DE) matrices and count matrices, a collection of functions for manipulating and plotting data via 'ggplot2', and functions to work with cell graphs and cell embeddings. Graph-based methods include embedding kNN cell graphs into a UMAP <doi:10.21105/joss.00861>, collapsing vertices of each cluster in the graph, and propagating graph labels.
Authors:
sccore_1.0.5.tar.gz
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sccore.pdf |sccore.html✨
sccore/json (API)
# Install 'sccore' in R: |
install.packages('sccore', repos = c('https://kharchenkolab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/kharchenkolab/sccore/issues
- cellAnnotations - Conos cell annotations
- conosClusterList - Conos clusters list
- conosGraph - Conos graph
- umapEmbedding - UMAP embedding
Last updated 9 months agofrom:66c72f5c33. Checks:OK: 9. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 22 2024 |
R-4.5-win-x86_64 | OK | Nov 22 2024 |
R-4.5-linux-x86_64 | OK | Nov 22 2024 |
R-4.4-win-x86_64 | OK | Nov 22 2024 |
R-4.4-mac-x86_64 | OK | Nov 22 2024 |
R-4.4-mac-aarch64 | OK | Nov 22 2024 |
R-4.3-win-x86_64 | OK | Nov 22 2024 |
R-4.3-mac-x86_64 | OK | Nov 22 2024 |
R-4.3-mac-aarch64 | OK | Nov 22 2024 |
Exports:adjacent_vertex_weightsadjacentVerticesappendSpecificityMetricsToDEas_factorcheckPackageInstalledcollapseCellsByTypecollapseGraphPagacollapseGraphSumcolSumByFactorcomputeChebyshevCoeffsdotPlotembeddingColorsPlotembeddingGroupPlotembeddingPlotembedGraphUmapembedKnnGraphextendMatrixfac2colfac2paletteget_nearest_neighborsgetClusterGraphgraphToAdjListheatFilterjsDistmergeCountMatricesmulti2dendplapplypropagate_labelspropagateLabelspropagateLabelsDiffusionpropagateLabelsSolversaveDeAsJsonsetMinMaxsmooth_count_matrixsmoothChebyshevsmoothSignalOnGraphsnsplitVectorByNodesstyleEmbeddingPlotval2colval2ggcol
Dependencies:BHclicolorspacecpp11dplyrdqrngfansifarverFNNgenericsggplot2ggrepelgluegtableigraphirlbaisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepbmcapplypillarpkgconfigplyrpROCR6RColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppProgressrlangRSpectrascalessitmotibbletidyselectutf8uwotvctrsviridisLitewithr