Queries the Human Cell Atlas

Documentation for package ‘cellNexus’ version 0.99.23

cellNexus-package	cellNexus: Query Interface for the Human Cell Atlas
cellNexus	cellNexus: Query Interface for the Human Cell Atlas
create_interface_app	Create a Shiny app that allows users to generate filtering & retreival code for cellNexus
get_atlas_versions	Returns the atlas version changelog as a tibble
get_cell_communication_strength	Retrieve cellNexus cell communication ligand–receptor strength as a data frame.
get_counts_per_million	Generating counts per million from a SingleCellExperiment object
get_default_cache_dir	Returns the default cache directory with a version number
get_metadata	Gets the CellNexus metadata as a data frame.
get_metadata_url	Returns the URLs for all metadata files
get_pseudobulk	Gets a Pseudobulk from curated metadata
get_seurat	Given a data frame of HCA metadata, returns a Seurat object corresponding to the samples in that data frame
get_SingleCellExperiment	Gets a SingleCellExperiment from curated metadata
get_single_cell_experiment	Gets a SingleCellExperiment from curated metadata
join_census_table	Join Census metadata to an existing data frame
keep_quality_cells	Keep high-quality cells based on QC columns
organize_inputs	Organize arbitrary Shiny inputs into a grid layout
pbmc3k_sce	Sample SingleCellExperiment Object
SAMPLE_DATABASE_URL	URL pointing to the sample metadata file, which is smaller and for test, demonstration, and vignette purposes only
ui_choices	Pre-computed UI Choices for Interface App