Man pages for jlaffy/scalop
Single Cell Analysis Operations
| add_to_dataframe | Join a dataframe and a named vector |
| aggr_dup_genes | Aggregate duplicate gene rows |
| aggr_gene_expr | log-Average expression of genes across all cells |
| alias2ensembl | FUNCTION_TITLE |
| alias2entrez | FUNCTION_TITLE |
| alias2refseq | FUNCTION_TITLE |
| alias2symbol | FUNCTION_TITLE |
| alias2ucsc | FUNCTION_TITLE |
| allowedExons | FUNCTION_TITLE |
| annomap | One-bar annotation ggplot |
| as_bulk | Convert sc-matrix to simulated bulk |
| as_bulk_samples | Convert sc-matrix to simulated bulk samples matrix |
| as_four_state_gbm | Convert 6-state to 4-state GBM scores |
| assign_bulk_states | Assign Samples to States by High- and Low -frequency of their... |
| baseScores | Basic Scoring of Matrix by Gene sigs |
| bin | Generate Equally-Sized Bins |
| binmatch | Control Signatures From Expression Bins |
| bootstrapped_state_fractions | Bootstrapped State Fractions |
| bootstrap_summary | Summary Statistics for Bootstrapped State Fractions |
| cluster.methods | agglomeration method in hierarchical clustering agglomeration... |
| colcenter | Center a matrix column-wise |
| coldetected | Number of non-zero values per column |
| col_subset | Keep columns whose names match a pattern |
| combine_group2_dea | Aggregate 'scalop::dea' output for one group against many in... |
| comply | Apply a Function to All Pairs of Elements in 'x' or Between... |
| cor.methods | Correlation method method for computing correlation... |
| cpm | Convert Counts to Counts-Per-Million (CPM) |
| dea | Differential Expression Analysis |
| dims | <dim> for many matrices |
| discrete_colours | The 297 discrete colours available across different... |
| dist.methods | distance metric method for computing distances from a matrix... |
| doubletCells | Identify potential doublet cells |
| enricher | Functional enrichments |
| ensembl2symbol | ensembl2symbol |
| entrez2alias | FUNCTION_TITLE |
| entrez2ensembl | FUNCTION_TITLE |
| entrez2refseq | FUNCTION_TITLE |
| entrez2symbol | FUNCTION_TITLE |
| entrez2ucsc | FUNCTION_TITLE |
| expr_housekeeping | Expression level of Housekeeping Genes |
| filter_signatures | Filter Out Lowly-Correlated Genes from Signature(s) |
| filter_sigs | Filter genes in sigs according to reference |
| fitBimodal | Fit a Bimodal Gaussian Distribution |
| flip | Flip the (nested) elements of a character vector (or list)... |
| foldchange | fold changes |
| frac_mito | Fraction of a Cell's Expression Level Coming From... |
| futurama | futurama, 12 Discrete Colours |
| GeneInfo | Get Genomic Information |
| geneLength | FUNCTION_TITLE |
| genericModel | FUNCTION_TITLE |
| get_ensembl | FUNCTION_TITLE |
| get_entrez | FUNCTION_TITLE |
| get_genes | FUNCTION_TITLE |
| getGRCh | Get hg19 or hg38 information from biomaRt |
| get_refseq | FUNCTION_TITLE |
| get_signatures | FUNCTION_TITLE |
| get_snn_graph_clusters | FUNCTION_TITLE |
| get_symbols | FUNCTION_TITLE |
| get_ucsc | FUNCTION_TITLE |
| ggDensity | FUNCTION_TITLE |
| ggmap | gmap wrapper |
| ggoutliers | Plot model and Outliers |
| ggpubr | ggpubr, 3 Discrete Colours |
| ggvolcano | Volcano plot |
| gmap | Plot A Heatmap with ggplot2 |
| graster | Plot A Heatmap with ggplot2 |
| grombine | Combine ggplot grobs or plots |
| grouped_reorder | Grouped Reorder and Ungroup |
| grouped_rowcenter | Center matrix rows by subsets of columns |
| hca | Hierarchical clustering analysis |
| headl | Left-hand head a matrix or dataframe |
| headr | Right-hand head a matrix or dataframe |
| hierarchy | Cell state hierarchy coordinates |
| hms_span | Subtract POSIXt Class Objects in HH:MM:SS Format |
| is_accnum | FUNCTION_TITLE |
| is_alias | FUNCTION_TITLE |
| is_annotation | FUNCTION_TITLE |
| is_ensembl | FUNCTION_TITLE |
| is_entrez | FUNCTION_TITLE |
| is_refseq | FUNCTION_TITLE |
| is_symbol | FUNCTION_TITLE |
| is_ucsc | FUNCTION_TITLE |
| jaccard | Compute Jaccard Similarities between Pairs of Character... |
| jacFilt | Filter List By Jaccard |
| jacmap | Convert a list to a jaccard matrix and plot with... |
| ldcast | Turn a list into a dataframe |
| logcpm | Convert CPM to logCPM |
| logRowMeans | Row Means of Log2 data |
| map_alias | FUNCTION_TITLE |
| map_ensembl | FUNCTION_TITLE |
| map_entrez | FUNCTION_TITLE |
| map_genes | FUNCTION_TITLE |
| map_refseq | FUNCTION_TITLE |
| map_symbol | FUNCTION_TITLE |
| markerScores | Score a Matrix with Marker Gene Sets Of Normal Cell Types |
| Markers_Normal | Marker gene sets of Normal Cell Types and Pan-Cancer Programs |
| mat01 | Character List to Binary (membership) Matrix |
| maxcol_strict | Strict Column Assign |
| metaprograms | Compute Metaprograms |
| MGH136 | Glioblastoma patient MGH136 |
| msigdb | FUNCTION_TITLE |
| ncols | <ncol> for many matrices |
| NormalBrainSignatures2 | 98 Signatures for Normal Brain Cell Types |
| NormalBrainSignatures3 | 178 Signatures for Normal Brain Cell Types |
| NormalSignatures | 205 Signatures for Normal Cell Types |
| nrows | <nrow> for many matrices |
| nSigGenes | FUNCTION_TITLE |
| ntop | Select top n elements |
| ohmyqc | Quality control statistics for single cell RNA seq data |
| ohmySNNclusters | SNN Graph-Based Clustering |
| ohmytsne | A plot-friendly output for the Barnes-Hut implementation of... |
| outliers | FUNCTION_TITLE |
| overlap | FUNCTION_TITLE |
| pairup | List combinations |
| pal19 | pal19, 19 Pretty Discrete Colours |
| pal28 | pal28, 28 Pretty Discrete Colours |
| palG34R | palG34R, a palette of reds and blues for cases within two... |
| pca | Principal Component Analysis |
| pipe | Pipe operator |
| plot_hierarchy | Plot State Hierarchy (Quadrant plot) |
| programs | Find cell clusters and retrieve significant expresion... |
| range_rowmeans | Range of the rowMeans of a matrix |
| refseq2alias | FUNCTION_TITLE |
| refseq2ensembl | FUNCTION_TITLE |
| refseq2entrez | FUNCTION_TITLE |
| refseq2symbol | FUNCTION_TITLE |
| refseq2ucsc | FUNCTION_TITLE |
| rowcenter | Center a matrix row-wise |
| rowdetected | Number of non-zero values per row |
| row_subset | Keep rows whose names match a pattern |
| sample_strict | Assign Rows and Sample |
| Sapply | sapply wrapper |
| scdata | scRNA-seq data from a patient with Glioblastoma |
| score | Score matrix columns for groups of rows |
| setColNames | Set the colnames in an object |
| setRowNames | Set the rownames in an object |
| sigScores | Score a Matrix by Gene sigs (Signatures) |
| simpsons | simpsons, 16 Discrete Colours |
| state_fractions | State Fractions (by group) |
| state_high_genes | Genes Associated with High Frequency of a Cellular State |
| subsplit | Split a vector, list, matrix or dataframe into into a list of... |
| substri | Extract substrings between delimiters by position |
| symbol2alias | FUNCTION_TITLE |
| symbol2ensembl | FUNCTION_TITLE |
| symbol2entrez | FUNCTION_TITLE |
| symbol2refseq | FUNCTION_TITLE |
| symbol2ucsc | FUNCTION_TITLE |
| taill | Left-hand tail a matrix or dataframe |
| tailr | Right-hand tail a matrix or dataframe |
| theme_scalop | FUNCTION_TITLE |
| totalExons | FUNCTION_TITLE |
| tpm | Convert logTPM to TPM |
| ucsc2alias | FUNCTION_TITLE |
| ucsc2ensembl | FUNCTION_TITLE |
| ucsc2entrez | FUNCTION_TITLE |
| ucsc2refseq | FUNCTION_TITLE |
| ucsc2symbol | FUNCTION_TITLE |
| unique_sample_names | Get unique sample names |
| Unlist | Unlist, keeping original list or element names |
| unlogcpm | Convert logCPM to CPM |
| unlogtpm | Convert TPM to logTPM |
| unpack-assign | Destructuring assignment |
| unpack-assign-back | Destructuring assignment |
| vannomap | One-bar annotation ggplot |
| which_annotation | FUNCTION_TITLE |
| wilcoxtest | wilcoxon-tests |
| x2y | FUNCTION_TITLE |
