Classifier for Single-cell RNA-seq Using Cell Clusters

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Documentation for package ‘clustifyr’ version 1.0.0

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assign_ident manually change idents as needed
average_clusters Average expression values per cluster
binarize_expr Binarize scRNAseq data
calculate_pathway_gsea Convert expression matrix to GSEA pathway scores (would take a similar place in workflow before average_clusters/binarize)
calc_similarity compute similarity
call_consensus get concensus calls for a list of cor calls
call_to_metadata Insert called ident results into metadata
cbmc_m reference marker matrix from seurat citeseq CBMC tutorial
cbmc_ref reference matrix from seurat citeseq CBMC tutorial
clustify Compare scRNA-seq data to reference data.
clustify.default Compare scRNA-seq data to reference data.
clustify.Seurat Compare scRNA-seq data to reference data.
clustify.seurat Compare scRNA-seq data to reference data.
clustify.SingleCellExperiment Compare scRNA-seq data to reference data.
clustifyr_methods Correlation functions available in clustifyr
clustify_lists Main function to compare scRNA-seq data to gene lists.
clustify_lists.default Main function to compare scRNA-seq data to gene lists.
clustify_lists.Seurat Main function to compare scRNA-seq data to gene lists.
clustify_lists.seurat Main function to compare scRNA-seq data to gene lists.
clustify_lists.SingleCellExperiment Main function to compare scRNA-seq data to gene lists.
clustify_nudge Combined function to compare scRNA-seq data to bulk RNA-seq data and marker list
clustify_nudge.default Combined function to compare scRNA-seq data to bulk RNA-seq data and marker list
clustify_nudge.Seurat Combined function to compare scRNA-seq data to bulk RNA-seq data and marker list
clustify_nudge.seurat Combined function to compare scRNA-seq data to bulk RNA-seq data and marker list
collapse_to_cluster From per-cell calls, take highest freq call in each cluster
compare_lists Calculate adjusted p-values for hypergeometric test of gene lists or jaccard index
cor_to_call get best calls for each cluster
cor_to_call_rank get ranked calls for each cluster
cor_to_call_topn get top calls for each cluster
cosine Cosine distance
downrefs table of references stored in clustifyrdata
downsample_matrix downsample matrix by cluster or completely random
feature_select_PCA Returns a list of variable genes based on PCA
file_marker_parse takes files with positive and negative markers, as described in garnett, and returns list of markers
find_rank_bias Find rank bias
gene_pct pct of cells in each cluster that express genelist
gene_pct_markerm pct of cells in every cluster that express a series of genelists
get_best_match_matrix Function to make best call from correlation matrix
get_best_str Function to make call and attach score
get_common_elements Find entries shared in all vectors
get_similarity Compute similarity of matrices
get_unique_column Generate a unique column id for a dataframe
get_vargenes Generate variable gene list from marker matrix
gmt_to_list convert gmt format of pathways to list of vectors
insert_meta_object more flexible metadata update of single cell objects
kl_divergence KL divergence
marker_select decide for one gene whether it is a marker for a certain cell type
matrixize_markers Convert candidate genes list into matrix
not_pretty_palette black and white palette for plotting continous variables
object_data Function to access object data
object_data.Seurat Function to access object data
object_data.seurat Function to access object data
object_data.SingleCellExperiment Function to access object data
object_loc_lookup lookup table for single cell object structures
object_ref Function to convert labelled object to avg expression matrix
object_ref.default Function to convert labelled object to avg expression matrix
object_ref.Seurat Function to convert labelled object to avg expression matrix
object_ref.seurat Function to convert labelled object to avg expression matrix
object_ref.SingleCellExperiment Function to convert labelled object to avg expression matrix
overcluster Overcluster by kmeans per cluster
overcluster_test compare clustering parameters and classification outcomes
parse_loc_object more flexible parsing of single cell objects
pbmc_markers Marker genes identified by Seurat from single-cell RNA-seq PBMCs.
pbmc_markers_M3Drop Marker genes identified by M3Drop from single-cell RNA-seq PBMCs.
pbmc_matrix_small Matrix of single-cell RNA-seq PBMCs.
pbmc_meta Meta-data for single-cell RNA-seq PBMCs.
pbmc_vargenes Variable genes identified by Seurat from single-cell RNA-seq PBMCs.
percent_clusters Percentage detected per cluster
permute_similarity Compute a p-value for similarity using permutation
plot_best_call Plot best calls for each cluster on a tSNE or umap
plot_call Plot called clusters on a tSNE or umap, for each reference cluster given
plot_cor Plot similarity measures on a tSNE or umap
plot_cor_heatmap Plot similarity measures on heatmap
plot_dims Plot a tSNE or umap colored by feature.
plot_gene Plot gene expression on to tSNE or umap
plot_pathway_gsea plot GSEA pathway scores as heatmap, returns a list containing results and plot.
pos_neg_marker generate pos and negative marker expression matrix from a list/dataframe of positive markers
pos_neg_select adapt clustify to tweak score for pos and neg markers
pretty_palette Color palette for plotting continous variables
pretty_palette2 Color palette for plotting continous variables, starting at gray
pretty_palette_ramp_d Expanded color palette ramp for plotting discrete variables
ref_feature_select feature select from reference matrix
ref_marker_select marker selection from reference matrix
reverse_marker_matrix generate negative markers from a list of exclusive positive markers
run_gsea Run GSEA to compare a gene list(s) to per cell or per cluster expression data
sce_small Small SingleCellExperiment object
seurat_meta Function to convert labelled seurat object to fully prepared metadata
seurat_meta.Seurat Function to convert labelled seurat object to fully prepared metadata
seurat_meta.seurat Function to convert labelled seurat object to fully prepared metadata
seurat_ref Function to convert labelled seurat object to avg expression matrix
seurat_ref.Seurat Function to convert labelled seurat object to avg expression matrix
seurat_ref.seurat Function to convert labelled seurat object to avg expression matrix
s_small Small clustered Seurat2 object
s_small3 Small clustered Seurat3 object
vector_similarity Compute similarity between two vectors
write_meta Function to write metadata to object
write_meta.Seurat Function to write metadata to object
write_meta.seurat Function to write metadata to object
write_meta.SingleCellExperiment Function to write metadata to object