scplode 0.1.0

scplode: a memory-efficient fast accesser for adata files

scplode

"Scplode" your disk space once and get faster access to your single cell data with less memory.

Why scplode?

• Disk space is cheap. Time and memory are not.
• A one-time index pays dividends in faster data access
• Familiar read_h5ad() and indexing commands for seamless data exploration

How it compares

Tool	Pros	Cons
Backed AnnData	Full-featured	Slower access times
BioNeMo	Similar memory mapping	Heavier weight, unfamiliar API
scplode	Fast, memory-efficient, familiar API	Requires disk space for index

Installation

pip install scplode

Quick Start

import scplode as sp

# Your familiar workflow, now faster
adata = sp.read_h5ad('your_data.h5ad')

Examples

Located in examples directory:

• 00_example: Demonstrates use of scplode, and tests for equivalent results
• 01_benchmark: Compares scplode and anndata for random and contiguous indexing
• 02_state_benchmark: Compares scplode and anndata when using scplode with the Arc Institute State Model

Requirements

• Python 3.8+
• AnnData
• Pandas
• Numpy

License

MIT