Package: sccore 1.0.5

Evan Biederstedt

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:Viktor Petukhov [aut], Rasmus Rydbirk [aut], Peter Kharchenko [aut], Evan Biederstedt [aut, cre]

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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'))

Peer review:

Bug tracker:https://github.com/kharchenkolab/sccore/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

6.41 score 12 stars 9 packages 30 scripts 1.8k downloads 41 exports 49 dependencies

Last updated 9 months agofrom:66c72f5c33. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 23 2024
R-4.5-win-x86_64OKOct 23 2024
R-4.5-linux-x86_64OKOct 23 2024
R-4.4-win-x86_64OKOct 23 2024
R-4.4-mac-x86_64OKOct 23 2024
R-4.4-mac-aarch64OKOct 23 2024
R-4.3-win-x86_64OKOct 23 2024
R-4.3-mac-x86_64OKOct 23 2024
R-4.3-mac-aarch64OKOct 23 2024

Exports:adjacent_vertex_weightsadjacentVerticesappendSpecificityMetricsToDEas_factorcheckPackageInstalledcollapseCellsByTypecollapseGraphPagacollapseGraphSumcolSumByFactorcomputeChebyshevCoeffsdotPlotembeddingColorsPlotembeddingGroupPlotembeddingPlotembedGraphUmapembedKnnGraphextendMatrixfac2colfac2paletteget_nearest_neighborsgetClusterGraphgraphToAdjListheatFilterjsDistmergeCountMatricesmulti2dendplapplypropagate_labelspropagateLabelspropagateLabelsDiffusionpropagateLabelsSolversaveDeAsJsonsetMinMaxsmooth_count_matrixsmoothChebyshevsmoothSignalOnGraphsnsplitVectorByNodesstyleEmbeddingPlotval2colval2ggcol

Dependencies:BHclicolorspacecpp11dplyrdqrngfansifarverFNNgenericsggplot2ggrepelgluegtableigraphirlbaisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepbmcapplypillarpkgconfigplyrpROCR6RColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppProgressrlangRSpectrascalessitmotibbletidyselectutf8uwotvctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
List of adjacent vertex weights from igraph objectadjacent_vertex_weights
List of adjacent vertices from igraph objectadjacentVertices
Append specificity metrics to DEappendSpecificityMetricsToDE
convert character vector into a factor with names "values" and "levels"as_factor
Conos cell annotationscellAnnotations
Check whether a package is installed and suggest how to install from CRAN, Bioconductor, or other external sourcecheckPackageInstalled
Collapse count matrices by cell type, given min/max number of cellscollapseCellsByType
Collapse graph using PAGA 1.2 algorithm, Wolf et al 2019, Genome Biology (2019) <https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1663-x>collapseGraphPaga
Collapse Graph By SumcollapseGraphSum
Calculates factor-stratified sums for each columncolSumByFactor
Conos clusters listconosClusterList
Conos graphconosGraph
Dot plot adapted from Seurat:::DotPlot, see ?Seurat:::DotPlot for detailsdotPlot
Set colors for embedding plot. Used primarily in embeddingPlot().embeddingColorsPlot
Plotting function for cluster labels, names contain cell names. Used primarily in embeddingPlot().embeddingGroupPlot
Plot embedding with provided labels / colors using ggplot2embeddingPlot
Embed a graph into a UMAP, Uniform Manifold Approximation and Projection for Dimension Reduction, <https://github.com/lmcinnes/umap>, <doi:10.21105/joss.00861>embedGraphUmap
Embed a k-nearest neighbor (kNN) graph within a UMAP. Used within embedGraphUmap(). Please see McInnes et al <doi:10.21105/joss.00861> for the UMAP description and implementation.embedKnnGraph
Extend matrix to include new columns in matrixextendMatrix
Utility function to translate a factor into colorsfac2col
Encodes logic of how to handle named-vector and functional palettes. Used primarily within embeddingGroupPlot()fac2palette
Get nearest neighbors method on graphget_nearest_neighbors
Collapse vertices belonging to each cluster in a graphgetClusterGraph
Convert igraph graph into an adjacency listgraphToAdjList
Graph filter with the heat kernel: f(x) = exp(-beta |x / lambda_m - a|^b)heatFilter
Jensen–Shannon distance metric (i.e. the square root of the Jensen–Shannon divergence) between the columns of a dense matrix mjsDist
Merge list of count matrices into a common matrix, entering 0s for the missing entriesmergeCountMatrices
Translate multilevel segmentation into a dendrogram, with the lowest level of the dendrogram listing the cellsmulti2dend
Parallel, optionally verbose lapply. See ?parallel::mclapply for more info.plapply
Label propagationpropagate_labels
Estimate labeling distribution for each vertex, based on provided labels.propagateLabels
Estimate labeling distribution for each vertex, based on provided labels using a Random Walk on graphpropagateLabelsDiffusion
Propagate labels using Zhu, Ghahramani, Lafferty (2003) algorithm, "Semi-Supervised Learning Using Gaussian Fields and Harmonic Functions" <http://mlg.eng.cam.ac.uk/zoubin/papers/zgl.pdf>propagateLabelsSolver
Save DE results as JSON tables for viewing in browsersaveDeAsJson
Set range for values in object. Changes values outside of range to min or max. Adapted from Seurat::MinMaxsetMinMax
Smooth gene expression, used primarily within conos::correctGenes. Used to smooth gene expression values in order to better represent the graph structure. Use diffusion of expression on graph with the equation dv = exp(-a * (v + b))smooth_count_matrix
Smooth Signal on GraphsmoothSignalOnGraph
Set names equal to values, a stats::setNames wrapper functionsn
splitVectorByNodessplitVectorByNodes
Set plot.theme, legend, ticks for embedding plot. Used primarily in embeddingPlot().styleEmbeddingPlot
UMAP embeddingumapEmbedding
Utility function to translate values into colors.val2col
Helper function to return a ggplot color gradient for a numeric vector ggplot(aes(color=x, ...), ...) + val2ggcol(x)val2ggcol