ArticleGigaScience2026
GEfetch2R: fetching single-cell/bulk RNA-seq data from public repositories to R and benchmarking the subsequent format conversion tools.
Article in GigaScience, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
2 citing papers in PubMed.
- GEfetch2R: fetching single-cell/bulk RNA-seq data from public repositories to R and benchmarking the subsequent format conversion tools.GigaScience · 2026Article
- Celline: a flexible tool for one-step retrieval and integrative analysis of public single-cell RNA sequencing data.Frontiers in bioinformatics · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
backgroundDownloading and reanalyzing the existing single-cell RNA sequencing (scRNA-seq) data provides an efficient choice to gain clues and new insights. However, no tool can fetch the diverse scRNA-seq data types (raw data, count matrix, and processed object) distributed in various repositories, process and load the downloaded data to R, convert formats between scRNA-seq objects, and benchmark the format conversion tools.
findingsHere, we present GEfetch2R, an R package with Docker image to (i) download diverse scRNA-seq data types, including raw data (SRA and ENA), count matrix (GEO, UCSC Cell Browser, and PanglaoDB), and processed objects (GEO, Zenodo, CELLxGENE, and HCA); (ii) process the downloaded data, load the count matrices/annotations/rds files to R (SeuratObject/DESeqDataSet), filter the SeuratObject based on cell metadata and genes, and dissect and extract the RData files; and (iii) convert formats between the widely used scRNA-seq objects, including SeuratObject, AnnData, SingleCellExperiment, CellDataSet/cell_data_set, and loom, and benchmark format conversion tools in terms of information kept, usability, running time, and scalability to guide the tool selection. Furthermore, GEfetch2R can also download, process, and load bulk RNA-seq raw data (SRA and ENA) and count matrices (GEO) to R (DESeqDataSet).
conclusionsGEfetch2R is an R package that facilitates researchers in accessing and exploring existing gene expression data from various public repositories. It can function as a data downloader (supports all 3 scRNA-seq and 2 bulk RNA-seq data types), a data processor (processes and loads the output/downloaded count matrices and annotations to R), and an object format converter (between the widely used scRNA-seq objects).
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.