ShennongObject: Modern Data Structures for Multi-Omics Analysis

The goal of ShennongObject is to provide an S4 class, Shennong, designed for storing and analyzing multi-modal single-cell and bulk omics data. It builds upon the MultiAssayExperiment framework, offering a structured way to manage multiple assays (e.g., RNA, ATAC), data layers within assays (e.g., counts, normalized data, scaled data), dimensional reductions (e.g., PCA, UMAP), sample metadata, and analysis provenance.

The design of ShennongObject was inspired by the structured API of the Seurat package for single-cell data, and draws conceptual influence from the tidyomics philosophy to support tidyverse-style workflows for omics analysis.

Installation

To install the development version from GitHub:

# install.packages("pak")
pak::pak("zerostwo/shennong-object")

Quick Start Example

This is a basic example showing how to create a Shennong object:

library(ShennongObject)

# 1. Create dummy RNA counts matrix (genes x samples)
genes <- paste0("Gene", 1:100)
samples <- paste0("Sample", 1:10)
rna_counts <- matrix(
  rpois(1000, lambda = 10),
  nrow = 100,
  dimnames = list(genes, samples)
)
# Make it sparse for demonstration
rna_counts[sample(1000, 300)] <- 0
rna_counts <- as(rna_counts, "dgCMatrix")

# 2. Create dummy sample metadata
sample_metadata <- data.frame(
  condition = sample(c("Control", "Treated"), 10, replace = TRUE),
  batch = factor(sample(c("A", "B"), 10, replace = TRUE)),
  row.names = samples
)

# 3. Create the Shennong object
sn_obj <- sn_initialize_shennong_object(
  counts = rna_counts,
  metadata = sample_metadata,
  project = "QuickStart",
  assay = "RNA" # Name for the primary assay
)

# Print basic summary
print(sn_obj)
#> A Shennong object:  QuickStart 
#> Organism: NA 
#> A Shennong object of 1 listed
#>  experiment with a user-defined name and respective class.
#>  Containing an ExperimentList class object of length 1:
#>  [1] RNA: SummarizedExperiment with 100 rows and 10 columns
#> Functionality:
#>  experiments() - obtain the ExperimentList instance
#>  colData() - the primary/phenotype DataFrame
#>  sampleMap() - the sample coordination DataFrame
#>  `$`, `[`, `[[` - extract colData columns, subset, or experiment
#>  *Format() - convert into a long or wide DataFrame
#>  assays() - convert ExperimentList to a SimpleList of matrices
#>  exportClass() - save data to flat files
#> 
#> --- Shennong Specific Slots ---
#> Active Assay: RNA 
#> Active Ident: 1 levels (first few: QuickStart ) 
#> 0 dimensional reduction(s) present: None 
#> Misc data: None 
#> Command history stored: No 
#> Tools data stored: None 
#> Object created with ShennongObject version: 0.1.0

For more detailed usage, please see the package vignettes, starting with the “Quick Start Guide”:

Code of Conduct

Please note that the ShennongObject project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.