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
MarioniLab/DropletUtils documentation built on Nov. 12, 2023, 6:13 a.m.