Index

A

adata (quadsv.detectors.irregular.DetectorIrregular attribute) align_spectra_by_rotation() (in module quadsv.comparators.multisample)

apply_rotations_to_spectra() (in module quadsv.comparators.multisample) auto_chunk_size() (in module quadsv.statistics)

B

backend_ (quadsv.detectors.irregular.DetectorIrregular attribute)

C

centering (quadsv.kernels.base.Kernel attribute) Comparator() (in module quadsv.api) ComparatorGrid (class in quadsv.comparators.grid) ComparatorIrregular (class in quadsv.comparators.irregular) compare_glm() (in module quadsv.comparators.multisample) compare_two_groups() (in module quadsv.comparators.multisample) compare_two_groups_masked() (in module quadsv.comparators.multisample) compare_two_groups_scalar() (in module quadsv.comparators.multisample) compute_null_params() (in module quadsv.statistics)

compute_qstat() (quadsv.detectors.base.Detector method) (quadsv.detectors.grid.DetectorGrid method) (quadsv.detectors.irregular.DetectorIrregular method) compute_rstat() (quadsv.detectors.base.Detector method) (quadsv.detectors.grid.DetectorGrid method) (quadsv.detectors.irregular.DetectorIrregular method) compute_sample_spectrum() (in module quadsv.comparators.multisample) compute_torus_distance_matrix() (in module quadsv.utils) convert_visium_to_physical() (in module quadsv.utils) coords (quadsv.kernels.nufft.NUFFTKernel attribute)

D

Detector (class in quadsv.detectors.base) Detector() (in module quadsv.api)

DetectorGrid (class in quadsv.detectors.grid) DetectorIrregular (class in quadsv.detectors.irregular)

E

effective_rank() (in module quadsv.statistics) eigenvalues() (quadsv.kernels.base.Kernel method) (quadsv.kernels.base.MatrixKernelBase method) (quadsv.kernels.fft.FFTKernel method) (quadsv.kernels.nufft.NUFFTKernel method)

estimate_rotations_from_landmarks() (in module quadsv.comparators.multisample)

F

feature_mode (quadsv.comparators.grid.ComparatorGrid attribute) (quadsv.comparators.irregular.ComparatorIrregular attribute) fft_solver (quadsv.kernels.fft.FFTKernel attribute) FFTKernel (class in quadsv.kernels.fft)

freq_edges (quadsv.comparators.grid.ComparatorGrid attribute) (quadsv.comparators.irregular.ComparatorIrregular attribute) from_coordinates() (quadsv.kernels.matrix.MatrixKernel class method) from_matrix() (quadsv.kernels.matrix.MatrixKernel class method)

G

gene_names (quadsv.comparators.grid.ComparatorGrid attribute) (quadsv.comparators.irregular.ComparatorIrregular attribute) gene_pattern_diversity() (in module quadsv.statistics)

get_rect_coords() (in module quadsv.utils) get_visium_coords() (in module quadsv.utils) grid_shape (quadsv.kernels.nufft.NUFFTKernel attribute)

K

Kernel (class in quadsv.kernels.base) kernel_ (quadsv.detectors.base.Detector attribute) kernel_method_ (quadsv.detectors.base.Detector attribute) kernel_params_ (quadsv.detectors.base.Detector attribute)

Kx() (quadsv.kernels.base.Kernel method) (quadsv.kernels.base.MatrixKernelBase method) (quadsv.kernels.fft.FFTKernel method) (quadsv.kernels.nufft.NUFFTKernel method) Kx_grid() (quadsv.kernels.nufft.NUFFTKernel method)

L

liu_sf() (in module quadsv.statistics)

load_visium_sample() (in module quadsv.utils)

M

MatrixKernel (class in quadsv.kernels.matrix) MatrixKernelBase (class in quadsv.kernels.base) method (quadsv.kernels.base.Kernel attribute) (quadsv.kernels.base.MatrixKernelBase attribute) (quadsv.kernels.fft.FFTKernel attribute) (quadsv.kernels.nufft.NUFFTKernel attribute) min_cells (quadsv.detectors.irregular.DetectorIrregular attribute) min_count (quadsv.detectors.grid.DetectorGrid attribute) module quadsv quadsv.api quadsv.comparators quadsv.comparators.base quadsv.comparators.grid quadsv.comparators.irregular quadsv.comparators.multisample quadsv.detectors quadsv.detectors.base quadsv.detectors.grid quadsv.detectors.irregular quadsv.kernels quadsv.kernels.base quadsv.kernels.fft quadsv.kernels.matrix quadsv.kernels.nufft quadsv.statistics quadsv.utils

N

n (quadsv.detectors.base.Detector attribute) (quadsv.kernels.base.Kernel attribute) (quadsv.kernels.base.MatrixKernelBase attribute) (quadsv.kernels.fft.FFTKernel attribute) (quadsv.kernels.nufft.NUFFTKernel attribute) n_grid (quadsv.kernels.fft.FFTKernel attribute)

n_rfft (quadsv.kernels.fft.FFTKernel attribute) normalize_background() (in module quadsv.comparators.multisample) normalize_covariates() (in module quadsv.comparators.multisample) normalize_shape() (in module quadsv.comparators.multisample) NUFFTKernel (class in quadsv.kernels.nufft) nx (quadsv.kernels.fft.FFTKernel attribute) ny (quadsv.kernels.fft.FFTKernel attribute)

P

params (quadsv.kernels.base.Kernel attribute) (quadsv.kernels.base.MatrixKernelBase attribute) (quadsv.kernels.fft.FFTKernel attribute) (quadsv.kernels.nufft.NUFFTKernel attribute)

power_spectrum_2d() (in module quadsv.kernels.fft) power_spectrum_2d_nufft() (in module quadsv.kernels.nufft)

Q

quadsv module quadsv.api module quadsv.comparators module quadsv.comparators.base module quadsv.comparators.grid module quadsv.comparators.irregular module quadsv.comparators.multisample module quadsv.detectors module quadsv.detectors.base module

quadsv.detectors.grid module quadsv.detectors.irregular module quadsv.kernels module quadsv.kernels.base module quadsv.kernels.fft module quadsv.kernels.matrix module quadsv.kernels.nufft module quadsv.statistics module quadsv.utils module

R

radial_bin_spectrum() (in module quadsv.comparators.multisample)

realization() (quadsv.kernels.base.MatrixKernelBase method)

S

samples (quadsv.comparators.grid.ComparatorGrid attribute) (quadsv.comparators.irregular.ComparatorIrregular attribute) sdata (quadsv.detectors.grid.DetectorGrid attribute) setup_data() (quadsv.detectors.base.Detector method) (quadsv.detectors.grid.DetectorGrid method) (quadsv.detectors.irregular.DetectorIrregular method) spacing (quadsv.kernels.nufft.NUFFTKernel attribute) spatial_q_test() (in module quadsv.statistics)

spatial_r_test() (in module quadsv.statistics) spectrum (quadsv.kernels.fft.FFTKernel attribute) square_trace() (quadsv.kernels.base.Kernel method) (quadsv.kernels.base.MatrixKernelBase method) (quadsv.kernels.fft.FFTKernel method) (quadsv.kernels.nufft.NUFFTKernel method) stores_precision (quadsv.kernels.base.MatrixKernelBase attribute) (quadsv.kernels.nufft.NUFFTKernel attribute)

T

topology (quadsv.kernels.fft.FFTKernel attribute) trace() (quadsv.kernels.base.Kernel method) (quadsv.kernels.base.MatrixKernelBase method) (quadsv.kernels.fft.FFTKernel method) (quadsv.kernels.nufft.NUFFTKernel method)

V

visium_hex_spacing_um() (in module quadsv.utils)

visium_to_grid() (in module quadsv.utils) VISIUM_V1_SPOT_SPACING_UM (in module quadsv.utils)

W

within_group_pattern_diversity() (in module quadsv.statistics)

workers (quadsv.kernels.fft.FFTKernel attribute) (quadsv.kernels.nufft.NUFFTKernel attribute)

X

xtKx() (quadsv.kernels.base.Kernel method) (quadsv.kernels.base.MatrixKernelBase method) (quadsv.kernels.fft.FFTKernel method) (quadsv.kernels.nufft.NUFFTKernel method) xtKx_matmul() (quadsv.kernels.nufft.NUFFTKernel method)

xtKx_standardized() (quadsv.kernels.base.MatrixKernelBase method) xtKy() (quadsv.kernels.base.Kernel method) (quadsv.kernels.base.MatrixKernelBase method) (quadsv.kernels.fft.FFTKernel method) (quadsv.kernels.nufft.NUFFTKernel method) xtKy_matmul() (quadsv.kernels.nufft.NUFFTKernel method)