BrentLab/rossi_2021

Rossi 2021

This data is gathered from yeastepigenome.org. This work was published in

Rossi MJ, Kuntala PK, Lai WKM, Yamada N, Badjatia N, Mittal C, Kuzu G, Bocklund K, Farrell NP, Blanda TR, Mairose JD, Basting AV, Mistretta KS, Rocco DJ, Perkinson ES, Kellogg GD, Mahony S, Pugh BF. A high-resolution protein architecture of the budding yeast genome. Nature. 2021 Apr;592(7853):309-314. doi: 10.1038/s41586-021-03314-8. Epub 2021 Mar 10. PMID: 33692541; PMCID: PMC8035251.

Accessing Data

The examples below require labretriever (pip install labretriever) and/or the HuggingFace Hub client (pip install huggingface_hub).

Accessing Data with labretriever

This repository is part of a collection configured as a unified database using labretriever.VirtualDB. Download the collection config and use it to query the data directly in Python, or with an AI assistant using the labretriever plugin.

from labretriever.virtual_db import VirtualDB
from labretriever.datacard import DataCard

# Citation and metadata
card = DataCard("BrentLab/rossi_2021")
info = card.info()
print(info["doi"])
print(info["citation"])

# path to the downloaded brentlab_yeast_collection.yaml
vdb = VirtualDB("/path/to/brentlab_yeast_collection.yaml")

print(vdb.get_dataset_description("rossi"))
vdb.query("SELECT * FROM rossi LIMIT 5")

Direct parquet access

The repository contains more data than what is exposed through the collection configuration. Use DataCard.info() to inspect available files, then download and query with DuckDB.

Most files in this repository are single parquet files and can be read directly:

from huggingface_hub import snapshot_download
import duckdb

repo_path = snapshot_download(
    repo_id="BrentLab/rossi_2021",
    repo_type="dataset",
    allow_patterns="rossi_2021_af_combined.parquet",
)
conn = duckdb.connect()
# returns a pandas DataFrame with the first 5 rows
conn.execute(
    "SELECT * FROM read_parquet(?) LIMIT 5",
    [f"{repo_path}/rossi_2021_af_combined.parquet"],
).df()

Accessing using R

Clone the repository and read parquet files directly with arrow:

# install.packages("arrow")
arrow::read_parquet("rossi_2021_af_combined.parquet")