API for MarioniLab/DropletUtils
Utilities for Handling Single-Cell Droplet Data
| Global functions | |
|---|---|
| .ambient_contrib_maximum | Source code |
| .ambient_contrib_negative | Source code |
| .ambient_contrib_sparse | Source code |
| .ambient_profile_bimodal | Source code |
| .ambient_profile_empty | Source code |
| .barcode_ranks | Source code |
| .check_for_compressed | Source code |
| .check_indices | Source code |
| .clean_tag_counts | Source code |
| .compute_ambient_stats | Source code |
| .compute_multinom_prob_data | Source code |
| .compute_multinom_prob_rest | Source code |
| .default_drops | Source code |
| .empty_drops | Source code |
| .empty_drops_cell_ranger | Source code |
| .estimate_alpha | Source code |
| .extract_mol_info | Source code |
| .find_curve_bounds | Source code |
| .get_cell_ordering | Source code |
| .get_lower_dist | Source code |
| .get_putative_empty | Source code |
| .hashed_drops | Source code |
| .intColSums | Source code |
| .maximum_ambience | Source code |
| .maximum_ambience_loop | Source code |
| .parallelize | Source code |
| .permute_counter | Source code |
| .read_from_hdf5 | Source code |
| .read_from_sparse | Source code |
| .realize_DA_to_memory | Source code |
| .reindex_mol_info_features | Source code |
| .remap_quantiles | Source code |
| .remove_ambience | Source code |
| .reorder | Source code |
| .report_ambient_profile | Source code |
| .rounded_to_integer | Source code |
| .safe_good_turing | Source code |
| .setup_pcg_state | Source code |
| .tenx_loader | Source code |
| .test_empty_drops | Source code |
| .type_chooser | Source code |
| .unmask_barcode | Source code |
| .write_hdf5 | Source code |
| .write_sparse | Source code |
| .write_stripped_mol_info | Source code |
| ambientContribMaximum | Man page |
| ambientContribMaximum,ANY-method | Man page |
| ambientContribMaximum,SummarizedExperiment-method | Man page |
| ambientContribNegative | Man page |
| ambientContribNegative,ANY-method | Man page |
| ambientContribNegative,SummarizedExperiment-method | Man page |
| ambientContribSparse | Man page |
| ambientContribSparse,ANY-method | Man page |
| ambientContribSparse,SummarizedExperiment-method | Man page |
| ambientProfileBimodal | Man page |
| ambientProfileBimodal,ANY-method | Man page |
| ambientProfileBimodal,SummarizedExperiment-method | Man page |
| ambientProfileEmpty | Man page |
| ambientProfileEmpty,ANY-method | Man page |
| ambientProfileEmpty,SummarizedExperiment-method | Man page |
| barcodeRanks | Man page |
| barcodeRanks,ANY-method | Man page |
| barcodeRanks,SummarizedExperiment-method | Man page |
| chimericDrops | Man page Source code |
| cleanTagCounts | Man page |
| cleanTagCounts,ANY-method | Man page |
| cleanTagCounts,SummarizedExperiment-method | Man page |
| controlAmbience | Man page Source code |
| defaultDrops | Man page |
| defaultDrops,ANY-method | Man page |
| defaultDrops,SummarizedExperiment-method | Man page |
| downsampleBatches | Man page |
| downsampleMatrix | Man page |
| downsampleReads | Man page Source code |
| downsample_run | Source code |
| downsample_run_per_cell | Source code |
| emptyDrops | Man page |
| emptyDrops,ANY-method | Man page |
| emptyDrops,SummarizedExperiment-method | Man page |
| emptyDropsCellRanger | Man page |
| emptyDropsCellRanger,ANY-method | Man page |
| emptyDropsCellRanger,SummarizedExperiment-method | Man page |
| encodeSequences | Man page Source code |
| encode_sequences | Source code |
| estimateAmbience | Man page Source code |
| find_chimeric | Source code |
| find_swapped | Source code |
| get10xMolInfoStats | Man page Source code |
| get_cell_barcodes | Source code |
| group_cells | Source code |
| hashedDrops | Man page |
| hashedDrops,ANY-method | Man page |
| hashedDrops,SummarizedExperiment-method | Man page |
| hashed_constant | Source code |
| hashed_deltas | Source code |
| inferAmbience | Man page Source code |
| inv.which | Source code |
| makeCountMatrix | Man page Source code |
| maximumAmbience | Man page Source code |
| montecarlo_pval | Source code |
| read10xCounts | Man page Source code |
| read10xMolInfo | Man page Source code |
| reexports | Man page |
| removeAmbience | Man page |
| removeAmbience,ANY-method | Man page |
| removeAmbience,SummarizedExperiment-method | Man page |
| removeChimericDrops | Man page Source code |
| removeSwappedDrops | Man page Source code |
| simBasicMolInfo | Source code |
| simCounts | Source code |
| simSwappedMolInfo | Source code |
| swappedDrops | Man page Source code |
| testEmptyDrops | Man page Source code |
| write10xCounts | Man page Source code |
