# Queries the Human Cell Atlas

## Documentation for package ‘cellNexus’ version 0.99.23

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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