Pepkio Knowledge Explorer: Single-Cell Long-Read RNA Sequencing

Install a pip package to load single-cell long-read RNA sequencing knowledge graphs, benchmark Q&A, and the static explorer from Python scripts, notebooks, or CI—without cloning a repository.

What It Does

This package provides programmatic access to the knowledge graph and benchmark Q&A for single-cell long-read RNA sequencing (scLR-seq), isoform analysis, and long-read bioinformatics. Data are synthesized and extracted from seven source papers and bundled as knowledge.json, benchmark.json, and the same HTML/JS/CSS files as the static web app.

Use it to query papers, concepts, tools, and relationships in code, export filtered benchmark subsets for LLM evaluation, or serve the interactive explorer locally.

Features

• Load and query papers, concepts, tools, relationships, and benchmark[] from bundled JSON
• Filter and export benchmark Q&A as JSON or CSV for LLM/agent evaluation
• CLI: info, benchmark export, serve for local static hosting
• Bundled static web app (same files as pepkio/kg-single-cell-long-read-rna-sequencing)
• Offline use — no API key required

Installation

pip install pepkio-kg-single-cell-long-read-rna-sequencing

Quick Example

from pepkio_kg_single_cell_long_read_rna_sequencing import KnowledgeExplorer

explorer = KnowledgeExplorer.load()
print(f"Benchmark questions: {len(explorer.benchmark)}")  # 34
explorer.export_benchmark("tools_benchmark.csv", format="csv", category="Tools")

CLI:

pepkio-kg-single-cell-long-read-rna-sequencing info
pepkio-kg-single-cell-long-read-rna-sequencing benchmark export -o benchmark.json
pepkio-kg-single-cell-long-read-rna-sequencing serve --port 8766

Bundled dataset (version 0.1.0): 7 papers, 46 concepts, 72 tools, 34 benchmark questions across categories Benchmarking (7), Tools (7), Methods (6), Concepts (7), Platforms (7), and difficulties beginner (12), intermediate (13), advanced (9).

Typical Use Cases

• RAG evaluation with field-specific questions and ground-truth answers tied to source papers
• Agent benchmarking pipelines in CI that score model responses against exported CSV subsets
• Teaching scripts that reference structured paper metadata and concept relationships
• Local exploration via serve without cloning the GitHub static app repository

Scientific Background

Single-cell long-read RNA sequencing applies PacBio HiFi or Oxford Nanopore platforms to droplet-based libraries (10x Genomics, MAS-ISO-seq, Kinnex), reading full-length cDNA per cell for isoform-resolved transcriptomics. The bundled graph covers platform benchmarks, barcode detection, UMI clustering, isoform quantification tools (wf-single-cell, Bambu, Sicelore, BLAZE), and allele-specific expression—topics where short-read scRNA-seq cannot reliably resolve splice variants.

Web Application

For a graphical interface, use the hosted interactive explorer:

GitHub Pages: https://pepkio.github.io/kg-single-cell-long-read-rna-sequencing/

The companion editorial article at https://www.pepkio.com/blogs/articles/single-cell-long-read-rna-sequencing synthesizes the underlying benchmark literature with evidence-based platform comparisons and pipeline recommendations.

The web app adds a mind tree, Cytoscape knowledge graph, guided learning path (21 steps), Sankey ecosystem diagram, and benchmark export UI with category/difficulty filters.

Documentation and Resources

PyPI package source: https://github.com/pepkio/pepkio-kg-single-cell-long-read-rna-sequencing

Static app repository: https://github.com/pepkio/kg-single-cell-long-read-rna-sequencing

Companion blog article: https://www.pepkio.com/blogs/articles/single-cell-long-read-rna-sequencing

About Pepkio

Pepkio develops software tools, curated research knowledge resources, and bioinformatics analysis services for life science researchers.

Keywords

single-cell long-read RNA sequencing, scLR-seq, isoform-resolved scRNA-seq, PacBio HiFi single-cell, Oxford Nanopore single-cell, MAS-ISO-seq, Kinnex, 10x Genomics long-read, alternative splicing, novel isoform discovery, allele-specific expression, wf-single-cell, Bambu, Sicelore, BLAZE, flexiplex, FLAMES, LongBench, knowledge graph bioinformatics, benchmark Q&A dataset, LLM evaluation genomics, RAG ground-truth answers, Python knowledge explorer, pip install benchmark data, single-cell transcriptomics tools, long-read bioinformatics benchmark, isoform quantification Nanopore, cell barcode detection long-read, Pepkio knowledge explorer, structured paper metadata RNA-seq, export benchmark JSON CSV, offline genomics knowledge package, agent benchmarking life sciences, teaching single-cell isoform analysis, PacBio vs Nanopore single-cell comparison, Nanopore R10.4.1 single-cell pipeline, differential transcript usage long-read, full-length single-cell RNA sequencing, scRNA-seq long reads Python API, programmatic knowledge graph query, serve static explorer locally, single-cell long-read sequencing evaluation set, bioinformatics concept graph transcriptomics, ground-truth Q&A single-cell genomics, isoform validation RT-PCR benchmark, UMI clustering long-read tools, spatial long-read RNA-seq concepts, EPI2ME single-cell workflow, single-cell isoform quantification Python, knowledge graph export for ML pipelines