Man pages for MissionBio/tapestriR
Analysis of Data Generated by the Tapestri Platform
| add_analysis_layer | Add additional layers of analysis to Tapestri_Assay Object. |
| add_assay | Add Assay Object to Multiomics object (moo) |
| add_data_layer | Add additional layers of data to Tapestri_Assay Object |
| clr_by_cell | CLR normalization by cell |
| clr_by_feature | CLR normalization by feature |
| compute_ploidy | Identify ploidy for samples |
| create_assay | Create Tapestri_Assay Object |
| create_moo | Create Multiomics Object |
| define_subclones | define subclones based on NGT values |
| filter_variants | Filter raw genotypes based on quality |
| log_colMeans | Log normalization factor per feature |
| log_norm_by_cell | Log normalization by cell |
| log_norm_by_feature | Log normalization by feature |
| normalize_dna_reads | Normalize barcode data |
| read_assay_h5 | Read Tapestri multi-omics h5 file |
| read_insights_export | Read variant assay from data exported from Tapestri Insights |
| read_loom | Read loom file created by Tapestri pipeline |
| read_tap | read a tap file generated by Tapestri pipeline |
| recode_genotypes | Recode NGT values HET, HOM, WT or MUT/WT if zygosity is... |
| subset_assay | Subset assay |
| Tapestri_Assay-class | Tapestri_Assay class |
| Tapestri_Multiomics-class | The Tapestri_Multiomics Class |
| tapestri_ploidy_plot | Calculate ploidy |
| TapestriR | CNV analysis of Tapestri data |
| tapestri_scatterplot | Scatter plot wrapper for ggplots that makes plotting Tapestri... |
| tapestri_violinplot | violin plot wrapper for ggplots that makes plotting Tapestri... |
| umap_theme | Simple theme to show axis-less projection of umaps |
| validate_variant_annotations | Annotate Variants based on variant ID field |
