pycisTopic
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pycisTopic
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A
add_annotation() (in module pycisTopic.loom)
add_cell_data() (pycisTopic.cistopic_class.CistopicObject method)
add_clusterings() (in module pycisTopic.loom)
add_LDA_model() (pycisTopic.cistopic_class.CistopicObject method)
add_markers() (in module pycisTopic.loom)
add_metrics() (in module pycisTopic.loom)
add_region_data() (pycisTopic.cistopic_class.CistopicObject method)
B
binarize_topics() (in module pycisTopic.topic_binarization)
C
calculate_distance_join() (in module pycisTopic.gene_activity)
calculate_distance_with_limits_join() (in module pycisTopic.gene_activity)
calculate_peaks_and_extend() (in module pycisTopic.iterative_peak_calling)
call_peak() (pycisTopic.pseudobulk_peak_calling.MACSCallPeak method)
cell_topic_heatmap() (in module pycisTopic.clust_vis)
change_chromosome_source_in_bed() (in module pycisTopic.gene_annotation)
CistopicImputedFeatures (class in pycisTopic.diff_features)
CistopicObject (class in pycisTopic.cistopic_class)
collapse_duplicates() (in module pycisTopic.utils)
compute_kde() (in module pycisTopic.qc)
compute_qc_stats() (in module pycisTopic.qc)
compute_topic_metrics() (in module pycisTopic.topic_qc)
coord_to_region_names() (in module pycisTopic.utils)
cpm() (in module pycisTopic.iterative_peak_calling)
create_cistopic_object() (in module pycisTopic.cistopic_class)
create_cistopic_object_from_fragments() (in module pycisTopic.cistopic_class)
create_cistopic_object_from_matrix_file() (in module pycisTopic.cistopic_class)
create_pyranges_from_polars_df() (in module pycisTopic.fragments)
cross_entropy() (in module pycisTopic.topic_binarization)
D
df_to_named_matrix() (in module pycisTopic.loom)
E
export_gene_activity_to_loom() (in module pycisTopic.loom)
export_minimal_loom_gene() (in module pycisTopic.loom)
export_pseudobulk() (in module pycisTopic.pseudobulk_peak_calling)
export_region_accessibility_to_loom() (in module pycisTopic.loom)
extend_pyranges() (in module pycisTopic.gene_activity)
extend_pyranges_with_limits() (in module pycisTopic.gene_activity)
F
fig2img() (in module pycisTopic.utils)
filter_fragments_by_cb() (in module pycisTopic.fragments)
find_clusters() (in module pycisTopic.clust_vis)
find_diff_features() (in module pycisTopic.diff_features)
find_highly_variable_features() (in module pycisTopic.diff_features)
find_most_likely_chromosome_source_in_bed() (in module pycisTopic.gene_annotation)
G
gene_set_to_signature() (in module pycisTopic.signature_enrichment)
get_all_gene_annotation_ensembl_biomart_dataset_names() (in module pycisTopic.gene_annotation)
get_barcodes_passing_qc_for_sample() (in module pycisTopic.qc)
get_biomart_dataset_name_for_species() (in module pycisTopic.gene_annotation)
get_cbs_passing_filter() (in module pycisTopic.fragments)
get_chrom_sizes_and_alias_mapping_from_file() (in module pycisTopic.gene_annotation)
get_chrom_sizes_and_alias_mapping_from_ncbi() (in module pycisTopic.gene_annotation)
get_chrom_sizes_and_alias_mapping_from_ucsc() (in module pycisTopic.gene_annotation)
get_consensus_peaks() (in module pycisTopic.iterative_peak_calling)
get_fragments_in_peaks() (in module pycisTopic.fragments)
get_fragments_per_cb() (in module pycisTopic.fragments)
get_gene_activity() (in module pycisTopic.gene_activity)
get_insert_size_distribution() (in module pycisTopic.fragments)
get_log2_fc() (in module pycisTopic.diff_features)
get_metadata() (in module pycisTopic.loom)
get_ncbi_assembly_accessions_for_species() (in module pycisTopic.gene_annotation)
get_otsu_threshold() (in module pycisTopic.qc)
get_region_signature() (in module pycisTopic.pyGREAT)
get_regulons() (in module pycisTopic.loom)
get_tss_annotation_from_ensembl() (in module pycisTopic.gene_annotation)
get_tss_matrix() (in module pycisTopic.utils)
get_tss_profile() (in module pycisTopic.tss_profile)
get_wilcox_test_pvalues() (in module pycisTopic.diff_features)
gini() (in module pycisTopic.utils)
gini_coefficient() (in module pycisTopic.topic_qc)
H
harmony() (in module pycisTopic.clust_vis)
histogram_and_bin_centers() (in module pycisTopic.topic_binarization)
I
impute_accessibility() (in module pycisTopic.diff_features)
input_check() (in module pycisTopic.clust_vis)
intersection() (in module pycisTopic.genomic_ranges)
iterative_peak_filtering() (in module pycisTopic.iterative_peak_calling)
L
label_transfer() (in module pycisTopic.label_transfer)
label_transfer_coembedded() (in module pycisTopic.label_transfer)
load_narrow_peak() (pycisTopic.pseudobulk_peak_calling.MACSCallPeak method)
M
macs_call_peak() (in module pycisTopic.pseudobulk_peak_calling)
MACSCallPeak (class in pycisTopic.pseudobulk_peak_calling)
make_rankings() (pycisTopic.diff_features.CistopicImputedFeatures method)
markers() (in module pycisTopic.diff_features)
mean_axis1() (in module pycisTopic.diff_features)
merge() (in module pycisTopic.cistopic_class)
(pycisTopic.cistopic_class.CistopicObject method)
(pycisTopic.diff_features.CistopicImputedFeatures method)
module
pycisTopic.cistopic_class
pycisTopic.clust_vis
pycisTopic.diff_features
pycisTopic.fragments
pycisTopic.gene_activity
pycisTopic.gene_annotation
pycisTopic.genomic_ranges
pycisTopic.iterative_peak_calling
pycisTopic.label_transfer
pycisTopic.loom
pycisTopic.pseudobulk_peak_calling
pycisTopic.pyGREAT
pycisTopic.qc
pycisTopic.signature_enrichment
pycisTopic.topic_binarization
pycisTopic.topic_qc
pycisTopic.tss_profile
pycisTopic.utils
N
normalise_filepath() (in module pycisTopic.utils)
normalize_scores() (in module pycisTopic.diff_features)
O
overlap() (in module pycisTopic.genomic_ranges)
P
p_adjust_bh() (in module pycisTopic.diff_features)
peak_calling() (in module pycisTopic.pseudobulk_peak_calling)
plot_imputed_features() (in module pycisTopic.clust_vis)
plot_metadata() (in module pycisTopic.clust_vis)
plot_topic() (in module pycisTopic.clust_vis)
plot_topic_qc() (in module pycisTopic.topic_qc)
pycisTopic.cistopic_class
module
pycisTopic.clust_vis
module
pycisTopic.diff_features
module
pycisTopic.fragments
module
pycisTopic.gene_activity
module
pycisTopic.gene_annotation
module
pycisTopic.genomic_ranges
module
pycisTopic.iterative_peak_calling
module
pycisTopic.label_transfer
module
pycisTopic.loom
module
pycisTopic.pseudobulk_peak_calling
module
pycisTopic.pyGREAT
module
pycisTopic.qc
module
pycisTopic.signature_enrichment
module
pycisTopic.topic_binarization
module
pycisTopic.topic_qc
module
pycisTopic.tss_profile
module
pycisTopic.utils
module
pyGREAT() (in module pycisTopic.pyGREAT)
pyGREAT_oneset() (in module pycisTopic.pyGREAT)
R
read_barcodes_file_to_polars_series() (in module pycisTopic.fragments)
read_bed_to_polars_df() (in module pycisTopic.fragments)
read_fragments_from_file() (in module pycisTopic.utils)
read_fragments_to_polars_df() (in module pycisTopic.fragments)
read_fragments_to_pyranges() (in module pycisTopic.fragments)
read_tss_annotation_from_bed() (in module pycisTopic.gene_annotation)
reduce_pyranges_b() (in module pycisTopic.gene_activity)
reduce_pyranges_with_limits_b() (in module pycisTopic.gene_activity)
region_names_to_coordinates() (in module pycisTopic.utils)
region_set_to_signature() (in module pycisTopic.signature_enrichment)
region_weights() (in module pycisTopic.gene_activity)
run_tsne() (in module pycisTopic.clust_vis)
run_umap() (in module pycisTopic.clust_vis)
S
signature_enrichment() (in module pycisTopic.signature_enrichment)
smooth_topics_distributions() (in module pycisTopic.topic_binarization)
subset() (pycisTopic.cistopic_class.CistopicObject method)
(pycisTopic.diff_features.CistopicImputedFeatures method)
subset_array_second_axis() (in module pycisTopic.diff_features)
T
threshold_otsu() (in module pycisTopic.topic_binarization)
threshold_yen() (in module pycisTopic.topic_binarization)
topic_annotation() (in module pycisTopic.topic_qc)
W
weighted_aggregation() (in module pycisTopic.gene_activity)
weighted_integration() (in module pycisTopic.clust_vis)
write_tss_annotation_to_bed() (in module pycisTopic.gene_annotation)
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