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.
Readme
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 |
imports | dplyr , ggplot2 , ggrepel , graphics , grDevices , igraph , irlba , magrittr , Matrix , methods , parallel , pbmcapply , pROC , Rcpp , rlang , scales , tibble , utils , uwot , withr |
suggests | ggrastr (>= 0.1.7) , rmumps , testthat |
depends | R (>= 3.5.0) |
linkingto | RcppArmadillo , RcppEigen , RcppProgress |
Contributors | Peter Kharchenko, Viktor Petukhov, Ramus Rydbirk |
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