assign_ident            manually change idents as needed
average_clusters        Average expression values per cluster
binarize_expr           Binarize scRNAseq data
calc_similarity         compute similarity
calculate_pathway_gsea
                        Convert expression matrix to GSEA pathway
                        scores (would take a similar place in workflow
                        before average_clusters/binarize)
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_lists          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
clustifyr_methods       Correlation functions available in clustifyr
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_loc_lookup       lookup table for single cell object structures
object_ref              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
s_small                 Small clustered Seurat2 object
s_small3                Small clustered Seurat3 object
sce_small               Small SingleCellExperiment object
seurat_meta             Function to convert labelled seurat object to
                        fully prepared metadata
seurat_ref              Function to convert labelled seurat object to
                        avg expression matrix
vector_similarity       Compute similarity between two vectors
write_meta              Function to write metadata to object
