seqout

Clients for seqout.org, which aggregates study metadata from GEO, SRA, ENA, DDBJ, ArrayExpress, GEA and GSA. Search across all of them, resolve an accession to its records in every archive, and read GEO supplementary files as counts matrices.

Python

uv add seqout | seqout.org/cli/python

R

pak::pak("saketlab/seqout/R") | seqout.org/cli/R |

Python

from seqout import connect

sq = connect()
sq.search("liver cancer scRNA", organism="Homo sapiens")
sq.get("GSE151530").samples

The package also installs a seqout command:

seqout search "liver cancer scRNA" --organism "Homo sapiens"
seqout show GSE151530

R

library(seqout)

con <- seqout_connect()
find_projects(con, keywords = "liver cancer scRNA", organism = "Homo sapiens")
project_samples(con, "GSE151530")

From a GEO accession to a single-cell matrix

Supplementary files are grouped into units that read as one matrix: a 10x triplet, a CellRanger .h5, an .h5ad, an .rds or a table. The manifest resolves them without downloading anything, and the donor covariates come from the same accession.

from seqout import seqout_counts

counts = seqout_counts(gse="GSE297547")
counts.manifest()                       
m = counts.matrix(sample="GSM8994520")  
counts.design                           

counts <- seqout_counts(con, "GSE297547")
manifest(counts)
m <- seqout_matrix(counts, sample = "GSM8994520")
sample_frame(project_samples(con, "GSE297547"))