Single cell studies

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The 'Single cell studies database' lists papers in single cell transcriptomics with several fields of manually curated metadata.

See this publication for details:

A curated database reveals trends in single cell transcriptomics
Valentine Svensson, Eduardo da Veiga Beltrame, & Lior Pachter
Database, Volume 2020, 2020, baaa073; doi: 10.1093/database/baaa073

A Google Sheets based GUI for the database can be accessed at https://nxn.se/single-cell-studies/gui.

Study missing or incorrect? Submit through this form: nxn.se/single-cell-studies/submit

A TSV version of the current state of the database can be downloaded from www.nxn.se/single-cell-studies/data.tsv

See these examples for programmatic access:

With Python

In [1]: import pandas as pd
In [2]: data = pd.read_csv('https://nxn.se/single-cell-studies/data.tsv', sep = '\t', storage_options = {'User-Agent': ''})

With R

> library(tidyverse)
> library(httr2)
> request('https://nxn.se/single-cell-studies/data.tsv') |> req_user_agent('') |> req_perform() |> resp_body_string() |> read_tsv() -> data

Accessing snapshots with gsutil

$ gsutil ls gs://single-cell-studies | tail
gs://single-cell-studies/data_snapshot_2019-08-06T08:00:00.tsv
gs://single-cell-studies/data_snapshot_2019-08-07T08:00:01.tsv
gs://single-cell-studies/data_snapshot_2019-08-10T08:00:04.tsv
gs://single-cell-studies/data_snapshot_2019-08-11T08:00:01.tsv
gs://single-cell-studies/data_snapshot_2019-08-12T08:00:06.tsv
gs://single-cell-studies/data_snapshot_2019-08-13T08:00:01.tsv
gs://single-cell-studies/data_snapshot_2019-08-14T08:00:06.tsv
gs://single-cell-studies/data_snapshot_2019-08-15T08:00:00.tsv
gs://single-cell-studies/data_snapshot_2019-08-16T08:00:01.tsv
gs://single-cell-studies/data_snapshot_2019-08-17T08:00:01.tsv

$ gsutil cp gs://single-cell-studies/data_snapshot_2019-08-17T08:00:01.tsv .
Copying gs://single-cell-studies/data_snapshot_2019-08-17T08:00:01.tsv...
/ [1 files][249.2 KiB/249.2 KiB]
Operation completed over 1 objects/249.2 KiB.