Man pages for dputhier/scigenex
The scigenex package (Single-Cell Informative GENe Explorer)

check_format_cluster_setCheck the format of a Clusterset object
ClusterSet-classClusterSet-class
cluster_set_from_matrixTransform any matrix and list into a ClusterSet object.
cluster_set_from_seuratTransform a Seurat objects / FindAllMarkers result into a...
cluster_set_reportCreate a report from a ClusterSet and Seurat object.
cluster_set_to_xlsWrite Cluster-Set gene lists into an excel sheet.
cluster_set_to_xls-ClusterSet-methodWrite Cluster-Set gene lists into an excel sheet.
cluster_statsCompute statistics about the clusters
cluster_stats-ClusterSet-methodCompute statistics about the clusters
clust_namesNames of gene clusters stored in the ClusterSet object
clust_names-ClusterSet-methodThe names of the gene clusters stored in the ClusterSet...
clust_sizeSizes of the clusters stored in a ClusterSet object...
clust_size-ClusterSet-methodSizes of the clusters stored in a ClusterSet object...
col_namesColumn names of an object
col_names-ClusterSet-methodColumn names of a ClusterSet object.
colors_for_gradientGenerate a vector of colors for a gradient
compare_genesetsCompare two lists of gene sets
complex9The Complex9 dataset A set of 2D points corresponding to 9...
complex9NoisyThe complex9Noisy dataset A noisy version of the complex9...
construct_new_graphConstruct a new graph for a ClusterSet object
create_3_rnd_clustGenerate an example dataset with three clusters of profiles
create_4_rnd_clustGenerate an example dataset with four clusters of profiles
create_rand_strGenerate a random string of letters and numbers
dim-ClusterSet-methodDimension of a ClusterSet object. dim
discrete_paletteGenerate a discrete color palette
display_hullDraw a hull around a region of interest of Visium data.
enrich_goEnrichment analysis using GO database of gene clusters from a...
enrich_go-ClusterSet-methodEnrichment analysis using GO database of gene clusters from a...
filter_by_dot_prodFilter cluster from a ClusterSet object using dot product.
filter_cluster_sdFilter out gene clusters with small standard deviation.
filter_cluster_sizeFilter out gene clusters containing few genes
filter_nb_supporting_cellsFilter out cluster supported by few cells.
gene_clusterThe gene clusters stored in a ClusterSet. gene_cluster
gene_cluster-ClusterSet-methodThe gene clusters stored in a ClusterSet. gene_cluster
gene_clusteringGene clustering using the Markov Cluster Algorithm (MCL)...
get_data_for_scigenexFetch an expression matrix from a file, dataframe or Seurat...
getFlippedTissueCoordinatesSeurat object internally store spot coordinates (see...
get_genesExtract genes list from each gene clusters.
get_verbosityGet the current verbosity level.
grapes-in-grapes-character-ClusterSet-methodMatch operator of a ClusterSet object
grep_clustSearch genes within ClusterSet using a REGEXP.
grep_clust-ClusterSet-methodSearch genes within ClusterSet using a REGEXP.
install_mclInstall MCL
keep_dbf_graphConstruct a graph based on selected genes in a ClusterSet...
load_example_datasetLoad/download a Seurat or ClusterSet example dataset.
lymph_node_selected_spotThe lymph_node_selected_spot dataset
lymph_node_selected_spot_2The lymph_node_selected_spot dataset (#2)
mcl_system_cmdCall MCL program for graph partitioning (internal).
module_quality_scoresCompute Gene Module Quality Scores
module_quality_scores-ClusterSet-methodCompute Gene Module Quality Scores
nclustNumber of clusters in a ClusterSet object. nclust
nclust-ClusterSet-methodNumber of clusters in a ClusterSet object. nclust
ncol.ClusterSetncol.ClusterSet
nrow.ClusterSetnrow.ClusterSet
plot_clust_enrichmentsPlot Cluster Enrichments
plot_clust_enrichments-ClusterSet-methodPlot Cluster Enrichments
plot_cluster_statsPlot the result of cluster_stats()
plot_cmp_genesetsPlot the result of compare_genesets
plot_distPlot Distribution of distances
plot_ggheatmapHeatmap of data contained in a ClusterSet object.
plot_ggheatmap-ClusterSet-methodHeatmap of data contained in a ClusterSet object.
plot_heatmapplot_heatmap
plot_markers_to_clustersMap cell markers to clusters (hypergeometric/jaccard)
plot_markers_to_clusters-ClusterSet-methodMap cell markers to clusters (hypergeometric/jaccard)
plot_profilesPlot mean expression profiles of each cluster from a...
plot_spatialXY scatter plot of Visium data with hexagonal spots.
plot_spatial_panelA planel of XY scatter plots of Visium data with hexagonal...
plot_stratumDisplay the results of stratify_seurat
print_msgPrint a message based on the level of verbosity
print_statDebugging statistics (vector, matrix or dataframe)
rename_clustRename the gene clusters of a ClusterSet
rename_clust-ClusterSet-methodRename the gene clusters of a ClusterSet
reorder_clustReorder the clusters from a ClusterSet
reorder_clust-ClusterSet-methodReorder the clusters from a ClusterSet
reorder_genesReorder genes in a ClusterSet object.
reorder_genes-ClusterSet-methodReorder genes in a ClusterSet object.
row_namesRow names of a ClusterSet object. row_names
row_names-ClusterSet-methodRow names of a ClusterSet object. row_names
select_genesSelects informative genes based on k-nearest neighbour...
set_verbositySet the verbosity level for the SciGeneX package
show-ClusterSet-methodThe show method of a ClusterSet.
show_methodsList the method for the ClusterSet object.
stratify_seuratGiven two spot groups, compute for each spot: (i) the...
sub-ClusterSet-ANY-ANY-ANY-methodSubsetting operator of a ClusterSet object Extract
top_by_goSelect top_genes based on go terms
top_by_go-ClusterSet-methodSelect top_genes based on go terms
top_genesMost co-expressed genes from each gene cluster
top_genes-ClusterSet-methodMost co-expressed genes from each gene cluster
viz_enrichVisualization of enrichment analyses results from a...
viz_enrich-ClusterSet-methodVisualization of enrichment analyses results from a...
which_clustWhich clusters contain a set of genes.
which_clust-ClusterSet-methodWhich clusters contain a set of genes.
dputhier/scigenex documentation built on May 31, 2024, 8:59 a.m.