Index

C

concordance_summary() (in module ncountr.crossplatform.concordance)

D

de() (in module ncountr) (in module ncountr.core.de)

de_concordance() (in module ncountr.crossplatform.concordance) de_results (ncountr.experiment.NanostringExperiment attribute), [1] (ncountr.NanostringExperiment attribute), [1]

E

export_counts() (in module ncountr.io.export)

export_de() (in module ncountr.io.export) export_qc() (in module ncountr.io.export)

F

fetch_geo() (in module ncountr.io.geo)

G

genes (ncountr.experiment.NanostringExperiment property) (ncountr.NanostringExperiment property) get_cell_markers() (in module ncountr.datasets)

get_gene_set() (in module ncountr) (in module ncountr.datasets) get_scaling_factors() (in module ncountr.core.normalize)

H

hk_counts (ncountr.experiment.NanostringExperiment attribute), [1] (ncountr.NanostringExperiment attribute), [1]

L

lane_info (ncountr.experiment.NanostringExperiment attribute), [1] (ncountr.NanostringExperiment attribute), [1]

list_gene_sets() (in module ncountr) (in module ncountr.datasets)

M

marker_composition_proxy() (in module ncountr.crossplatform.composition) module ncountr ncountr.core.de ncountr.core.normalize ncountr.core.pathway ncountr.core.qc ncountr.crossplatform.composition ncountr.crossplatform.concordance ncountr.crossplatform.correlation ncountr.datasets ncountr.io.export ncountr.io.geo ncountr.io.rcc ncountr.plotting.de_plots ncountr.plotting.heatmaps ncountr.plotting.pathway_plots ncountr.plotting.qc_plots

N

n_genes (ncountr.experiment.NanostringExperiment property) (ncountr.NanostringExperiment property) n_samples (ncountr.experiment.NanostringExperiment property) (ncountr.NanostringExperiment property) NanostringExperiment (class in ncountr) (class in ncountr.experiment) ncountr module ncountr.core.de module ncountr.core.normalize module ncountr.core.pathway module ncountr.core.qc module ncountr.crossplatform.composition module ncountr.crossplatform.concordance module ncountr.crossplatform.correlation module

ncountr.datasets module ncountr.io.export module ncountr.io.geo module ncountr.io.rcc module ncountr.plotting.de_plots module ncountr.plotting.heatmaps module ncountr.plotting.pathway_plots module ncountr.plotting.qc_plots module neg_counts (ncountr.experiment.NanostringExperiment attribute), [1] (ncountr.NanostringExperiment attribute), [1] normalize() (in module ncountr) (in module ncountr.core.normalize) normalized (ncountr.experiment.NanostringExperiment attribute), [1] (ncountr.NanostringExperiment attribute), [1]

P

parse_rcc() (in module ncountr) (in module ncountr.io.rcc) per_gene_correlation() (in module ncountr.crossplatform.correlation) per_sample_correlation() (in module ncountr.crossplatform.correlation) plot_heatmap() (in module ncountr.plotting.heatmaps)

plot_pathway_scores() (in module ncountr.plotting.pathway_plots) plot_qc() (in module ncountr.plotting.qc_plots) plot_volcano() (in module ncountr.plotting.de_plots) pos_counts (ncountr.experiment.NanostringExperiment attribute), [1] (ncountr.NanostringExperiment attribute), [1]

Q

qc() (in module ncountr) (in module ncountr.core.qc)

qc_results (ncountr.experiment.NanostringExperiment attribute), [1] (ncountr.NanostringExperiment attribute), [1]

R

raw_counts (ncountr.experiment.NanostringExperiment attribute), [1] (ncountr.NanostringExperiment attribute), [1]

read_rcc() (in module ncountr) (in module ncountr.io.rcc)

S

sample_meta (ncountr.experiment.NanostringExperiment attribute), [1] (ncountr.NanostringExperiment attribute), [1] samples (ncountr.experiment.NanostringExperiment attribute) (ncountr.experiment.NanostringExperiment property) (ncountr.NanostringExperiment attribute) (ncountr.NanostringExperiment property)

score_gene_set() (in module ncountr) (in module ncountr.core.pathway)

T

to_anndata() (in module ncountr) (in module ncountr.io.export)