Man pages for blaserlab/blaseRtools
R Tools for Blaser Lab Data Analysis
| add_cds_factor_columns | Add predefined sample-level cell metadata to cell data sets... |
| aggregate.Matrix | Compute summary statistics of a Matrix |
| Ape-class | An S4 class to hold genebank/APE file data. |
| Ape.DNA | Get the DNASringSet Slot from an Ape Object |
| Ape.fasta | Save an Ape Instance as a Fasta File |
| Ape.fimo | Run FIMO on Selected Ape Object Features |
| Ape.granges | Get the GRanges Slot from an Ape Object |
| Ape.save | Save an Ape Instance as a Genebank Format File |
| Ape.setFeatures | Set the FEATURES Slot of a GRanges Object |
| as.cell_data_set | Convert objects to Monocle3 'cell_data_set' objects |
| as.Seurat.extras | Convert single cell experiment to Seurat |
| bb_aggregate | Aggregate Single Cell Gene Expression |
| bb_align | Align a CDS object according to a metadata variable |
| bb_annotate_npc | Annotate a Plot using NPC Coordinates |
| bb_blind_images | Make a Copy of Image Files and Rename With File Hashes in... |
| bb_buff_granges | Clean Up Your GRanges Object |
| bb_cds_anno | Annotate a CDS by Label Transfer |
| bb_cds_heatmap | Make a Heatmap of Aggregated Gene Expressionf from a CDS |
| bb_cellchat | Infer Cell-Cell Communication |
| bb_cellchat_heatmap | Make a Complex Heatmap From a CellChat Object With Sensible... |
| bb_cellmeta | Get Cell Metadata |
| bb_cite_umap | Plot a UMAP Showing Cite-Seq Antibody Binding |
| bb_cluster_representation | Cluster Representation By Fisher Exact Test Per Cell |
| bb_cluster_representation2 | Cluster Representation By Regression Per Sample |
| bb_daseq | Calculate Differential Abundance Using DAseq |
| bb_doubletfinder | Use doubletfinder to model and mark doublets |
| bb_extract_msig | Extract MSIGDB Gene Sets |
| bb_fix_file_path | Convert windows filepath to linux-compatible. |
| bb_fragment_replacement | Replace The Path to a Fragment File In a Signac Object |
| bb_genebubbles | Create a Gene Bubble/Dot Plot |
| bb_gene_dotplot | Make a dotplot of gene expression by cell population |
| bb_gene_modules | A function to generate gene modules and add them to the Gene... |
| bb_gene_pseudotime | Plot expression of a gene or genes in pseudotime. |
| bb_gene_umap | Make a Plot of Gene Expression in UMAP Form |
| bb_gene_violinplot | Make a plot of gene expression in UMAP form |
| bb_goenrichment | Go Term Enrichment |
| bb_goscatter | Make a scatter plot of GO term associations |
| bb_gosummary | A function to reduce go terms by semantic similarity |
| bb_import_bw | Import a Big Wig File |
| bb_import_seacr_peaks | Import Peaks from SEACR |
| bb_load_tenx_h5 | Load a 10X Genomics H5 File and Return a CDS |
| bb_load_tenx_targz | Load 10X Data Into CDS |
| bb_loupeR | Create a Loupe File from a Cell Data Set |
| bb_make_ape_genomic | Make an Ape Genome Object |
| bb_make_ape_transcript | Make an Ape Transcriptome Object |
| bb_makeTrace | Construct a Trace object from a Signac Object or Granges... |
| bb_merge_narrowpeaks | A Function To Merge Replicate Narrow Peaks GRanges |
| bb_metafeature | A Function to Generate Data For Making MetaPlots |
| bb_monocle_ | Annotate Single cell Data Using Monocle3 |
| bb_monocle_regression | A function to perform regression on single cell data. |
| bb_monocle_regression_better | An Improved Function to Perform Regression on Single Cell... |
| bb_parseape | Parse a Genebank File and Construct an APE Object |
| bb_plotfootprint | Plot motif footprinting results |
| bb_plot_genes_in_pseudotime | Plots expression for one or more genes as a function of... |
| bb_plot_heatmap_colData | Plot SummarizedHeatmap colData |
| bb_plot_heatmap_colDendro | Plot a Heatmap Column Dendrogram |
| bb_plot_heatmap_colHighlight | Plot a Column Highlight |
| bb_plot_heatmap_main | Plot the Body of Heatmap |
| bb_plot_heatmap_rowData | Plot a SummarizedHeatmap rowData |
| bb_plot_heatmap_rowDendro | Plot a Heatmap Row Dendrogram |
| bb_plot_heatmap_rowHighlight | Plot a Row Highlight |
| bb_plot_rowData_col | A helper function to generate a data frame in the proper form... |
| bb_plot_trace_axis | Plot The X Axis From A Trace Object |
| bb_plot_trace_data | Plot The Trace Data From A Trace Object |
| bb_plot_trace_links | Plot The Link Data From A Trace Object |
| bb_plot_trace_model | Plot The Gene Model From A Trace Object |
| bb_plot_trace_peaks | Plot The peak Data From A Trace Object |
| bb_print_full_stats | Print out a stats report |
| bb_promoter_overlap | Calculate The Overlap Between Peaks and Promoters |
| bb_pseudobulk_mf | Run Multifactor Pseudobulk Analysis using Deseq2 |
| bb_pseudocells | Generate a CDS from Bulk RNA-seq data |
| bb_pseudotime | Learn Graph and Calculate Pseudotime |
| bb_qc | A function to run qc tests on cds objects. |
| bb_read_bam | Read Bam Files |
| bb_read_narrowpeak | A Function to Read In Narrow Peaks Files |
| bb_rejoin | Rejoin qc and doubletfinder data to a cds object |
| bb_remove_dupes | Remove rows that have duplicates in a given column |
| bb_rowmeta | Get Feature/Gene Metadata |
| bb_seurat_anno | A function to generate automated cell labelings with Seurat |
| bb_split_atac | Split Out Peaks Data |
| bb_split_citeseq | Split Antibody Capture Data into Alt Experiment |
| bb_tbl_to_coldata | A Function To Add Tibble Columns To Cell Metadata |
| bb_tbl_to_matrix | Convert a wide-form tibble a matrix |
| bb_tbl_to_rowdata | A Function To Add Tibble Columns To Feature Metadata |
| bb_triplecluster | A function to generate clusters from scRNA-seq data |
| bb_unblind_images | Rejoin Blinded Scores to Original File Names |
| bb_var_umap | A function to generate a UMAP with colors mapped to colData... |
| COMMENTS | Get the Comments Slot from an Ape Object |
| data_median_se | Generate median +/- se stat object for jitter ggplot |
| data_summary_mean_sd | Generate mean +/- sd stat object for jitter ggplot |
| data_summary_mean_se | Generate mean +/- se stat object for jitter ggplot |
| data_summary_median_iqr | Generate median +/- iqr stat object for jitter ggplot |
| data_summary_median_mad | Generate median +/- mad stat object for jitter ggplot |
| dMcast | Casts or pivots a long 'data frame' into a wide sparse matrix |
| FEATURES | Get the Features Slot from an Ape Object |
| filter_cds | Filter a CDS |
| geom_split_violin | geom_split_violin |
| granges_to_features | Format a GRanges Object as a Character Vector For Inclusion... |
| grapes-notin-grapes | Operators |
| ImageCatalog-class | An S4 Image Catalog |
| Image-class | An S4 Class for Holding Image Metadata |
| LearnGraph | Run 'link[monocle3]{learn_graph}' on a 'Seurat' object |
| LOCUS | Get the Locus Slot from an Ape Object |
| merge.Matrix | Merges two Matrices or matrix-like objects |
| normalize_batch | Noramalize a Data Table by Group and Batch |
| rBind.fill | Combine matrixes by row, fill in missing columns |
| se | Calculate standard error of the mean |
| SeuratWrappers-package | blaseRtools: R Tools for Blaser Lab Data Analysis |
| show-Ape-method | Show an Ape Object |
| show-Trace-method | Show a Trace Object |
| SummarizedHeatmap | An S4 Class for Holding Heatmap Data |
| Trace-class | An S4 class to Hold Genome Track Data |
| Trace.data | Get the Trace Data Slot from a Trace Object |
| Trace.gene_model | Get the gene_model Slot from a Trace Object |
| Trace.links | Get the Links Slot from a Trace Object |
| Trace.peaks | Get the peaks Slot from a Trace Object |
| Trace.plot_range | Get the plot_range Slot from a Trace Object |
| Trace.setData | Set the Trace Data Slot of a GRanges Object |
| Trace.setLinks | Set the Links Slot of a GRanges Object |
| Trace.setpeaks | Set the peaks Slot of a GRanges Object |
| Trace.setRange | Set the Plot Range Slot of a GRanges Object |
