Single Cell Omics Platform Functions

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Documentation for package ‘SCOPfunctions’ version 0.0.0.9000

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.countsperclus Compute counts per cluster
.dub_cutoff A subroutine of prep_intrahash_doub to compute number of doublet neighbours
.FoldChange.default Compute average log fold changes
DE_MAST_RE_seurat MAST differential expression test with random effect for Seurat object
f_VIF Compute Variance Inflation Factors for gene sets
geneset_embed Generate activity scores (embeddings) for a feature set in a sample matrix
geneset_embed_list_seurat Generate activity scores (embeddings) for a list of feature sets and add to a Seurat object
geneset_VIF Compute Variance Inflation Factors for gene sets
plot_barIdentGroup Generate barplot of identity group composition
plot_network make a network plot of a set of co-expressed features
plot_vlnGrid Make grid of violin plots
prep_HTO_q_area_plot Make an area plot of proportions of cells assigned to singlets, doublets, and negatives as a function of the positive.quantile provided to Seurat::HTODemux
prep_intrahash_doub Estimate intra-hashtag doublets by finding cells whose nearest neighbours are doublets
prep_qc_rna Perform QC on RNA, classifying cells as keepers or outliers to be filtered
remap Map dataframe column, vector, or list of vectors
utils_big_as.matrix Convert a large sparse matrix into a dense matrix without errors
utils_detachAllPkgs Detach all packages from current session
utils_detectCoresRAM Detect cores with RAM constraints
utils_dlFile Check if a file matches given hash, else download it and check again
utils_printObjectSizes Show the memory size of the top n objects
utils_saveMeta Save file with metadata
utils_verboseFnc Wrapper to make a function more verbose