Man pages for NCBI-Hackathons/RClusterCT
Classifier for Single-cell RNA-seq Using Cell Clusters

append_genesGiven a reference matrix and a list of genes, take the union...
assess_rank_biasFind rank bias
assign_identmanually change idents as needed
average_clustersAverage expression values per cluster
binarize_exprBinarize scRNAseq data
build_atlasFunction to combine records into single atlas
calc_similaritycompute similarity
calculate_pathway_gseaConvert expression matrix to GSEA pathway scores (would take...
call_consensusget concensus calls for a list of cor calls
call_to_metadataInsert called ident results into metadata
cbmc_mreference marker matrix from seurat citeseq CBMC tutorial
cbmc_refreference matrix from seurat citeseq CBMC tutorial
check_raw_countsGiven a count matrix, determine if the matrix has been either...
clustifyCompare scRNA-seq data to reference data.
clustify_listsMain function to compare scRNA-seq data to gene lists.
clustify_nudgeCombined function to compare scRNA-seq data to bulk RNA-seq...
clustifyr_methodsCorrelation functions available in clustifyr
clustifyr-packageclustifyr: Classifier for Single-cell RNA-seq Using Cell...
collapse_to_clusterFrom per-cell calls, take highest freq call in each cluster
compare_listsCalculate adjusted p-values for hypergeometric test of gene...
cor_to_callget best calls for each cluster
cor_to_call_rankget ranked calls for each cluster
cor_to_call_topnget top calls for each cluster
cosineCosine distance
downrefstable of references stored in clustifyrdata
downsample_matrixdownsample matrix by cluster or completely random
feature_select_PCAReturns a list of variable genes based on PCA
file_marker_parsetakes files with positive and negative markers, as described...
find_rank_biasFind rank bias
gene_pctpct of cells in each cluster that express genelist
gene_pct_markermpct of cells in every cluster that express a series of...
get_best_match_matrixFunction to make best call from correlation matrix
get_best_strFunction to make call and attach score
get_common_elementsFind entries shared in all vectors
get_similarityCompute similarity of matrices
get_ucsc_referenceBuild reference atlases from external UCSC cellbrowsers
get_unique_columnGenerate a unique column id for a dataframe
get_vargenesGenerate variable gene list from marker matrix
gmt_to_listconvert gmt format of pathways to list of vectors
human_genes_10xVector of human genes for 10x cellranger pipeline
insert_meta_objectmore flexible metadata update of single cell objects
install_clustifyr_appInstall all packages needed for shiny app
kl_divergenceKL divergence
make_comb_refmake combination ref matrix to assess intermixing
marker_selectdecide for one gene whether it is a marker for a certain cell...
matrixize_markersConvert candidate genes list into matrix
mouse_genes_10xVector of mouse genes for 10x cellranger pipeline
not_pretty_paletteblack and white palette for plotting continous variables
object_dataFunction to access object data
object_loc_lookuplookup table for single cell object structures
object_refFunction to convert labelled object to avg expression matrix
overclusterOvercluster by kmeans per cluster
overcluster_testcompare clustering parameters and classification outcomes
parse_loc_objectmore flexible parsing of single cell objects
pbmc_markersMarker genes identified by Seurat from single-cell RNA-seq...
pbmc_markers_M3DropMarker genes identified by M3Drop from single-cell RNA-seq...
pbmc_matrix_smallMatrix of single-cell RNA-seq PBMCs.
pbmc_metaMeta-data for single-cell RNA-seq PBMCs.
pbmc_vargenesVariable genes identified by Seurat from single-cell RNA-seq...
percent_clustersPercentage detected per cluster
permute_similarityCompute a p-value for similarity using permutation
plot_best_callPlot best calls for each cluster on a tSNE or umap
plot_callPlot called clusters on a tSNE or umap, for each reference...
plot_corPlot similarity measures on a tSNE or umap
plot_cor_heatmapPlot similarity measures on heatmap
plot_dimsPlot a tSNE or umap colored by feature.
plot_genePlot gene expression on to tSNE or umap
plot_pathway_gseaplot GSEA pathway scores as heatmap, returns a list...
plot_rank_biasQuery rank bias results
pos_neg_markergenerate pos and negative marker expression matrix from a...
pos_neg_selectadapt clustify to tweak score for pos and neg markers
pretty_paletteColor palette for plotting continous variables
pretty_palette2Color palette for plotting continous variables, starting at...
pretty_palette_ramp_dExpanded color palette ramp for plotting discrete variables
query_rank_biasQuery rank bias results
ref_feature_selectfeature select from reference matrix
ref_marker_selectmarker selection from reference matrix
reverse_marker_matrixgenerate negative markers from a list of exclusive positive...
run_clustifyr_appLaunch Shiny app version of clustifyr, may need to run...
run_gseaRun GSEA to compare a gene list(s) to per cell or per cluster...
sce_smallSmall SingleCellExperiment object
seurat_metaFunction to convert labelled seurat object to fully prepared...
seurat_refFunction to convert labelled seurat object to avg expression...
s_smallSmall clustered Seurat2 object
s_small3Small clustered Seurat3 object
vector_similarityCompute similarity between two vectors
write_metaFunction to write metadata to object
NCBI-Hackathons/RClusterCT documentation built on July 20, 2021, 3:15 p.m.