GCSanndataR

Overview

GCSanndataR is an R package that extends anndataR to provide Google Cloud Storage-backed AnnData functionality. This package allows users to work with AnnData objects stored in Google Cloud Storage without downloading the entire file, enabling efficient access to large single-cell datasets directly from the cloud.

Installation

# Install from GitHub
# remotes::install_github("mkanai/GCSanndataR")
install.packages("GCSanndataR", repos = c('https://mkanai.r-universe.dev', 'https://cloud.r-project.org'))
GCSanndataR::install_gcs_anndata()

Usage

Reading AnnData from Google Cloud Storage

library(GCSanndataR)

# Read an AnnData file from Google Cloud Storage
# This will automatically use GCSAnnData backend
gcs_adata <- read_h5ad("gs://my-bucket/my-file.h5ad")

# Access specific rows and columns
gcs_adata$X[1:10, 1:5]

# Access using names
gcs_adata$X[c("cell1", "cell2"), c("gene1", "gene2")]

Features

• Direct access to AnnData objects stored in Google Cloud Storage
• Lazy loading of data - only loads the parts of the file that are needed
• Compatible with the anndataR API

Requirements

• R >= 4.0.0
• anndataR
• reticulate >= 1.36.1
• Google Cloud Storage access configured

License

MIT