sainsc.io

This module contains functionality supporting reading data of different spatially-resolved transcriptomics technologies and file formats.

Attributes

VIZGEN_CTRLS	Patterns for Vizgen controls
XENIUM_CTRLS	Patterns for Xenium controls

Functions

read_StereoSeq(filepath, *[, resolution, gene_name, ...])	Read a Stereo-seq GEM file.
read_StereoSeq_bins(filepath[, bin_size, spatialdata, ...])	Read a Stereo-seq GEM file into bins.
read_VisiumHD(path, *[, gene_name, raw, n_threads])	Read a VisiumHD sample.
read_Vizgen(filepath, *[, binsize, remove_genes, ...])	Read a Vizgen transcripts file.
read_Xenium(filepath, *[, binsize, remove_features, ...])	Read a Xenium transcripts file.
read_gem_file(filepath, *[, sep, n_threads])	Read a GEM file into a DataFrame.
read_gem_header(filepath)	Read the metadata from the top of the GEM file.