sccore v0.1.2

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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.

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sccore

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, collapsing vertices of each cluster in the graph, and propagating graph labels.

Installation

To install the stable version from CRAN, use:

install.packages('sccore')

To install the latest version, use:

install.packages('devtools')
devtools::install_github('kharchenkolab/sccore')

Citation

If you find sccore useful for your publication, please cite:

Viktor Petukhov, Ramus Rydbirk, Peter Kharchenko and Evan Biederstedt
(2021). sccore: Core Utilities for Single-Cell RNA-Seq. R package
version 0.1.2. https://github.com/kharchenkolab/sccore

Functions in sccore

Name Description
conosGraph Conos graph
dotPlot Dot plot adapted from Seurat:::DotPlot, see ?Seurat:::DotPlot for details
extendMatrix Extend matrix to include new columns in matrix
embeddingPlot Plot embedding with provided labels / colors using ggplot2
propagateLabelsDiffusion Estimate labeling distribution for each vertex, based on provided labels using a Random Walk on graph
propagateLabels Estimate labeling distribution for each vertex, based on provided labels.
embeddingGroupPlot Plotting function for cluster labels, names contain cell names. Used primarily in embeddingPlot().
embeddingColorsPlot Set colors for embedding plot. Used primarily in embeddingPlot().
getClusterGraph Collapse vertices belonging to each cluster in a graph
setMinMax Set range for values in object. Changes values outside of range to min or max. Adapted from Seurat::MinMax
get_nearest_neighbors Get nearest neighbors method on graph
smoothChebyshev Smooth with Chebyshev Polynomials
sn Set names equal to values, a stats::setNames wrapper function
fac2col Utility function to translate a factor into colors
colSumByFac Calculates factor-stratified sums for each column
heatFilter Graph filter with the heat kernel: $$f(x) = exp(-\beta |x / \lambda_m - a|^b)$$
graphToAdjList Convert igraph graph into an adjacency list
jsDist Jensen<U+2013>Shannon distance metric (i.e. the square root of the Jensen<U+2013>Shannon divergence) between the columns of a dense matrix m
mergeCountMatrices Merge list of count matrices into a common matrix, entering 0s for the missing entries
fac2palette Encodes logic of how to handle named-vector and functional palettes. Used primarily within embeddingGroupPlot()
styleEmbeddingPlot Set plot.theme, legend, ticks for embedding plot. Used primarily in embeddingPlot().
umapEmbedding UMAP embedding
propagateLabelsSolver 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>
propagate_labels Label propagation
embedGraphUmap Embed a graph into a UMAP, Uniform Manifold Approximation and Projection for Dimension Reduction, <https://github.com/lmcinnes/umap>, <doi:10.21105/joss.00861>
splitVectorByNodes splitVectorByNodes
embedKnnGraph 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.
multi2dend Translate multilevel segmentation into a dendrogram, with the lowest level of the dendrogram listing the cells
val2ggcol Helper function to return a ggplot color gradient for a numeric vector ggplot(aes(color=x, ...), ...) + val2ggcol(x)
val2col Utility function to translate values into colors.
plapply Parallel, optionally verbose lapply. See ?parallel::mclapply for more info.
smooth_count_matrix 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))
smoothSignalOnGraph Smooth Signal on Graph
collapseGraphSum Collapse Graph By Sum
collapseGraphPaga 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>
as_factor convert character vector into a factor with names "values" and "levels"
cellAnnotations Conos cell annotations
adjacent_vertex_weights List of adjacent vertex weights from igraph object
adjacentVertices List of adjacent vertices from igraph object
appendSpecificityMetricsToDE Append specificity metrics to DE
conosClusterList Conos clusters list
computeChebyshevCoeffs Compute Chebyshev Coefficients
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Details

License GPL-3
Encoding UTF-8
LazyData true
RoxygenNote 7.1.1
LinkingTo Rcpp, RcppArmadillo, RcppProgress, RcppEigen
NeedsCompilation yes
SystemRequirements C++11
URL https://github.com/kharchenkolab/sccore
BugReports https://github.com/kharchenkolab/sccore/issues
Packaged 2021-02-20 10:11:55 UTC; evanbiederstedt
Repository CRAN
Date/Publication 2021-02-23 12:20:03 UTC

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