Index

_

__init__() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method) (missionbio.mosaic.sample.Sample method) (missionbio.mosaic.samplegroup.SampleGroup method)

_Assay (class in missionbio.mosaic.assay)

A

add_col_attr() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method) add_extension() (missionbio.mosaic.assay._Assay class method) (missionbio.mosaic.cnv.Cnv class method) (missionbio.mosaic.dna.Dna class method) (missionbio.mosaic.protein.Protein class method) add_layer() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method)

add_metadata() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method) add_row_attr() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method) amp_uniformity() (missionbio.mosaic.cnv.Cnv method) apply() (missionbio.mosaic.samplegroup.SampleGroup method) assay_scatter() (missionbio.mosaic.sample.Sample method) assays() (missionbio.mosaic.sample.Sample method)

B

barcodes() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method)

barplot() (missionbio.mosaic.samplegroup.SampleGroup method)

C

cell_uniformity() (missionbio.mosaic.cnv.Cnv method) cells_per_ab() (missionbio.mosaic.protein.Protein method) clipped_values() (in module missionbio.mosaic.utils) clone_vs_analyte() (missionbio.mosaic.sample.Sample method) cluster() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method) clustered_barcodes() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method) clustered_ids() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method)

Cnv (class in missionbio.mosaic.cnv) COLORS (in module missionbio.mosaic.constants) compute_ploidy() (missionbio.mosaic.cnv.Cnv method) copy() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method) create() (missionbio.mosaic.assay._Assay class method) (missionbio.mosaic.cnv.Cnv class method) (missionbio.mosaic.dna.Dna class method) (missionbio.mosaic.protein.Protein class method)

D

del_col_attr() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method) del_layer() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method) del_metadata() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method)

del_row_attr() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method) disable_logging() (in module missionbio.mosaic.utils) Dna (class in missionbio.mosaic.dna) drop() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method)

E

extend_docs() (in module missionbio.mosaic.utils)

F

feature_scatter() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method) filter_amplicons() (missionbio.mosaic.cnv.Cnv method)

filter_barcodes() (missionbio.mosaic.dna.Dna method) filter_variants() (missionbio.mosaic.dna.Dna method) filter_variants_consecutive() (missionbio.mosaic.dna.Dna method) find_clones() (missionbio.mosaic.dna.Dna method) find_relevant_variants() (missionbio.mosaic.dna.Dna method) fishplot() (missionbio.mosaic.samplegroup.SampleGroup method)

G

ga() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method) get_annotations() (missionbio.mosaic.dna.Dna method) get_attribute() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method) get_gene_names() (missionbio.mosaic.cnv.Cnv method) get_indexes() (in module missionbio.mosaic.utils) get_labels() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method) get_palette() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method)

get_row_ids() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method) get_scaling_factor() (missionbio.mosaic.protein.Protein method) get_signal_profile() (missionbio.mosaic.protein.Protein method) get_variant_bulk_metrics() (missionbio.mosaic.dna.Dna method) getassays() (missionbio.mosaic.samplegroup.SampleGroup method) group_by_genotype() (missionbio.mosaic.dna.Dna method) group_clusters() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method)

H

hasassay() (missionbio.mosaic.samplegroup.SampleGroup method) heatmap() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method) (missionbio.mosaic.sample.Sample method)

highlight_heatmap() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method)

I

ids() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method)

L

LABEL (in module missionbio.mosaic.constants)

load() (in module missionbio.mosaic.io) load_example_dataset() (in module missionbio.mosaic.io)

M

merge() (missionbio.mosaic.samplegroup.SampleGroup method) merge_assay() (missionbio.mosaic.samplegroup.SampleGroup method) merge_similar_clusters() (missionbio.mosaic.dna.Dna method) missionbio.mosaic.constants module missionbio.mosaic.io module

missionbio.mosaic.utils module module missionbio.mosaic.constants missionbio.mosaic.io missionbio.mosaic.utils

N

name_id_by_pos() (missionbio.mosaic.cnv.Cnv method) normalize_barcodes() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method)

normalize_reads() (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.protein.Protein method) NORMALIZED_READS (in module missionbio.mosaic.constants)

P

PALETTE (in module missionbio.mosaic.constants) pathscale() (missionbio.mosaic.dna.Dna method) PCA_LABEL (in module missionbio.mosaic.constants)

plot_ploidy() (missionbio.mosaic.cnv.Cnv method) plot_variant_correlation() (missionbio.mosaic.dna.Dna method) Protein (class in missionbio.mosaic.protein)

R

raw_counts() (missionbio.mosaic.sample.Sample method) raw_heatmaps() (missionbio.mosaic.sample.Sample method) read_data() (missionbio.mosaic.sample.Sample method) read_distribution() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method) READS (in module missionbio.mosaic.constants) reads_to_ab() (missionbio.mosaic.protein.Protein method) rename_labels() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method) rename_sample() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method) reset() (missionbio.mosaic.sample.Sample method) reset_ids() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method)

ridgeplot() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method) run_lda() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method) run_pca() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method) run_umap() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method)

S

Sample (class in missionbio.mosaic.sample) SampleGroup (class in missionbio.mosaic.samplegroup) samples() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method) save() (in module missionbio.mosaic.io) scale_data() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method) SCALED_LABEL (in module missionbio.mosaic.constants) scatterplot() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method) select_columns() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method) select_rows() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method) set_ids_from_cols() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method) set_labels() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method) set_palette() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method)

set_random_seed() (in module missionbio.mosaic.utils) set_selected_labels() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method) signature() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method) signaturemap() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method) sort_columns() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method) sort_ids() (missionbio.mosaic.dna.Dna method) sort_rows() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method) split() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method) (missionbio.mosaic.sample.Sample method) static_fig() (in module missionbio.mosaic.utils) stripplot() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method)

T

test_signature() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method)

to_zip() (in module missionbio.mosaic.io)

U

UMAP_LABEL (in module missionbio.mosaic.constants)

umaps() (missionbio.mosaic.sample.Sample method) update_coloraxis() (missionbio.mosaic.dna.Dna static method)

V

violinplot() (missionbio.mosaic.assay._Assay method) (missionbio.mosaic.cnv.Cnv method) (missionbio.mosaic.dna.Dna method) (missionbio.mosaic.protein.Protein method)