Package: sccore 1.0.7

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'))

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

Uses libs:
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:

On CRAN:

Conda:

cppopenmp

7.36 score 12 stars 10 packages 47 scripts 2.3k downloads 41 exports 43 dependencies

Last updated from:3953dfd9cc. Checks:11 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64NOTE214
linux-devel-x86_64NOTE217
source / vignettesOK252
linux-release-arm64NOTE199
linux-release-x86_64NOTE206
macos-release-arm64NOTE163
macos-release-x86_64NOTE307
macos-oldrel-arm64NOTE108
macos-oldrel-x86_64NOTE338
windows-develNOTE212
windows-releaseNOTE206
windows-oldrelNOTE195
wasm-releaseOK204

Exports:adjacent_vertex_weightsadjacentVerticesappendSpecificityMetricsToDEas_factorcheckPackageInstalledcollapseCellsByTypecollapseGraphPagacollapseGraphSumcolSumByFactorcomputeChebyshevCoeffsdotPlotembeddingColorsPlotembeddingGroupPlotembeddingPlotembedGraphUmapembedKnnGraphextendMatrixfac2colfac2paletteget_nearest_neighborsgetClusterGraphgraphToAdjListheatFilterjsDistmergeCountMatricesmulti2dendplapplypropagate_labelspropagateLabelspropagateLabelsDiffusionpropagateLabelsSolversaveDeAsJsonsetMinMaxsmooth_count_matrixsmoothChebyshevsmoothSignalOnGraphsnsplitVectorByNodesstyleEmbeddingPlotval2colval2ggcol

Dependencies:BHclicpp11dplyrdqrngfarverFNNgenericsggplot2ggrepelgluegtableigraphirlbaisobandlabelinglatticelifecyclemagrittrMatrixpbmcapplypillarpkgconfigpROCR6RColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppProgressrlangRSpectraS7scalessitmotibbletidyselectutf8uwotvctrsviridisLitewithr

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
embeddingPlot generic Plot embedding with provided labels / colors using ggplot2embeddingPlot embeddingPlot,ANY-method embeddingPlot,Seurat-method embeddingPlot-methods,ANY embeddingPlot-methods,Seurat
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