Index

_

__init__() (opennano.io.GeoMxProcessor method) (opennano.normalization.Normalization method) (opennano.qc.CountsQC method)

A

adata (opennano.qc.CountsQC attribute)

apply_vst_with_base_norm() (opennano.normalization.Normalization method)

C

calc_min_area() (opennano.qc.CountsQC method) calc_min_nuclei() (opennano.qc.CountsQC method) calc_percent_aligned() (opennano.qc.CountsQC method) calc_percent_saturation() (opennano.qc.CountsQC method) calc_percent_stitched() (opennano.qc.CountsQC method)

calc_percent_trimmed() (opennano.qc.CountsQC method) calc_total_reads() (opennano.qc.CountsQC method) check_metric() (opennano.qc.CountsQC method) CountsQC (class in opennano.qc) create_single_anndata() (opennano.io.GeoMxProcessor static method)

D

df (opennano.qc.CountsQC attribute)

F

filter_by_negativeProbes() (opennano.qc.CountsQC static method)

G

GeoMxProcessor (class in opennano.io)

M

module opennano.io opennano.normalization opennano.qc

N

neg_probe_indices (opennano.qc.CountsQC attribute) norm_CPM() (opennano.normalization.Normalization method) norm_log1p() (opennano.normalization.Normalization method)

norm_MedianRatio() (opennano.normalization.Normalization method) norm_Quantile() (opennano.normalization.Normalization method) norm_VST() (opennano.normalization.Normalization method) Normalization (class in opennano.normalization)

O

opennano.io module opennano.normalization module

opennano.qc module

P

parse_dcc_files() (opennano.io.GeoMxProcessor method) parse_geo_soft_metadata_with_identifier() (opennano.io.GeoMxProcessor static method) parse_metadata() (opennano.io.GeoMxProcessor method) parse_pkc_file() (opennano.io.GeoMxProcessor method) passed_rois (opennano.qc.CountsQC attribute)

plot_before_after_filtering() (opennano.qc.CountsQC method) plot_density() (opennano.normalization.Normalization method) plot_pca() (opennano.normalization.Normalization method) plot_qc_results() (opennano.qc.CountsQC method) process() (opennano.io.GeoMxProcessor method)

R

read_dcc_files() (opennano.io.GeoMxProcessor static method) read_pkc() (opennano.io.GeoMxProcessor static method)

roi_metadata (opennano.qc.CountsQC attribute) run_all_checks() (opennano.qc.CountsQC method)

V

variance() (opennano.normalization.Normalization method)

W

write() (opennano.qc.CountsQC method)