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singleCellHaystack (version 0.3.4)

Finding Needles (=differentially Expressed Genes) in Haystacks (=single Cell Data)

Description

Identification of differentially expressed genes (DEGs) is a key step in single-cell transcriptomics data analysis. 'singleCellHaystack' predicts DEGs without relying on clustering of cells into arbitrary clusters. Single-cell RNA-seq (scRNA-seq) data is often processed to fewer dimensions using Principal Component Analysis (PCA) and represented in 2-dimensional plots (e.g. t-SNE or UMAP plots). 'singleCellHaystack' uses Kullback-Leibler divergence to find genes that are expressed in subsets of cells that are non-randomly positioned in a these multi-dimensional spaces or 2D representations. For the theoretical background of 'singleCellHaystack' we refer to Vandenbon and Diez (Nature Communications, 2020) .

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Install

install.packages('singleCellHaystack')

Monthly Downloads

270

Version

0.3.4

License

MIT + file LICENSE

Maintainer

Alexis Vandenbon

Last Published

March 28th, 2021

Functions in singleCellHaystack (0.3.4)

dat.expression

Single cell RNA-seq dataset.
dat.tsne

Single cell tSNE coordingates.
get_D_KL

Calculates the Kullback-Leibler divergence between distributions.
get_grid_points

A function to decide grid points in a higher-dimensional space
extract_row_lgRMatrix

Returns a row of a sparse matrix of class lgRMatrix. Function made by Ben Bolker and Ott Toomet (see https://stackoverflow.com/questions/47997184/)
hclust_haystack_highD

Function for hierarchical clustering of genes according to their distribution in a higher-dimensional space.
get_log_p_D_KL

Estimates the significance of the observed Kullback-Leibler divergence by comparig to randomizations.
plot_gene_set_haystack

Visualizing the detection/expression of a set of genes in a 2D plot
hclust_haystack_raw

Function for hierarchical clustering of genes according to their distribution on a 2D plot.
get_density

Function to get the density of points with value TRUE in the (x,y) plot
get_D_KL_highD

Calculates the Kullback-Leibler divergence between distributions for the high-dimensional version of haystack().
plot_gene_haystack

Visualizing the detection/expression of a gene in a 2D plot
plot_gene_haystack_raw

Visualizing the detection/expression of a gene in a 2D plot
plot_gene_set_haystack_raw

Visualizing the detection/expression of a set of genes in a 2D plot
kmeans_haystack_raw

Function for k-means clustering of genes according to their distribution on a 2D plot.
get_parameters_haystack

Function that decides most of the parameters that will be during the "Haystack" analysis.
get_reference

Get reference distribution
kmeans_haystack_highD

Function for k-means clustering of genes according to their distribution in a higher-dimensional space.
get_dist_two_sets

Calculate the pairwise Euclidean distances between the rows of 2 matrices.
get_euclidean_distance

Calculate the Euclidean distance between x and y.
hclust_haystack

Function for hierarchical clustering of genes according to their expression distribution in 2D or multi-dimensional space
haystack_highD

The main Haystack function, for higher-dimensional spaces.
read_haystack

Function to read haystack results from file.
show_result_haystack

Shows the results of the 'haystack' analysis in various ways, sorted by significance. Priority of params is genes > p.value.threshold > n.
extract_row_dgRMatrix

Returns a row of a sparse matrix of class dgRMatrix. Function made by Ben Bolker and Ott Toomet (see https://stackoverflow.com/questions/47997184/)
default_bandwidth.nrd

Default function given by function bandwidth.nrd in MASS. No changes were made to this function.
haystack

The main Haystack function
kmeans_haystack

Function for k-means clustering of genes according to their expression distribution in 2D or multi-dimensional space
haystack_2D

The main Haystack function, for 2-dimensional spaces.
kde2d_faster

Based on the MASS kde2d() function, but heavily simplified; it's just tcrossprod() now.
write_haystack

Function to write haystack result data to file.
singleCellHaystack-package

singleCellHaystack: Finding Needles (=differentially Expressed Genes) in Haystacks (=single Cell Data)