datasets
Training and evaluation data, with the modality, task and licence stated up front. Listed live from the Hugging Face Hub.
RNAgym
🧬 RNAGym
Benchmark suite for RNA fitness & structure prediction
RNAGym brings together >1 M mutational fitness measurements and curated RNA structure datasets in a single place. This Hugging Face repo lets you:
Download fitness benchmark data
Download secondary structure benchmark data
Download tertiary structure benchmark data
Contents
Folder
Purpose
fitness_prediction/
All mutation-fitness assays
secondary_structure_prediction/
Secondary… See the full description on the dataset page: https://huggingface.co/datasets/Marks-lab/RNAgym.rna-downstream-tasks
GB.RNA Benchmark Datasets
mRNA related tasks
Translation efficiency prediction from Chu et al.(2024) [1]
3 cell lines: Muscle, pc3, HEK
input sequence: 5'UTR
10-fold cross-validation split
mRNA expression level prediction from Chu et al.(2024) [1]
3 cell lines: Muscle, pc3, HEK
input sequence: 5'UTR
10-fold cross-validation split
Mean ribosome load prediction from Sample et al. (2019) [2]
input sequence: 5'UTR
ouput: mean ribosome load
the original data… See the full description on the dataset page: https://huggingface.co/datasets/genbio-ai/rna-downstream-tasks.RNA_chemical_ribonanzae_coli_rnasrnaglib
Dataset Card for Dataset Name
This dataset contains the tasks provided by rnaglib, a benchmarking suite for RNA structure-function modelling.
Dataset Details
Dataset Description
This dataset is a Python package wrapping RNA benchmark datasets and tasks. Data access, preprocessing, and task-specific pipelines are implemented in code and not fully expressed through this metadata schema. See documentation at https://github.com/cgoliver/rnaglib.
Curated by:… See the full description on the dataset page: https://huggingface.co/datasets/luiswyss/rnaglib.rnacentral
RNAcentral
RNAcentral is a free, public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases representing a broad range of organisms and RNA types.
The development of RNAcentral is coordinated by European Bioinformatics Institute and is supported by Wellcome. Initial funding was provided by BBSRC.
Disclaimer
This is an UNOFFICIAL release of the RNAcentral by The… See the full description on the dataset page: https://huggingface.co/datasets/multimolecule/rnacentral.jump-cp-0016-labelfree-RNARNA_degradationrna-junctions-dbrnahl-saluki-human
Overview
mRNA half-life is a measure of the degradation rate of mRNA molecules. This experiment reports the time that the expression level of a transcript takes to decrease by half. The original data source aggregates 39 human and 27 mouse transcriptome wide datasets -- this dataset contains the human datasets. Several data preprocessing steps are taken, reported in the original paper. Half-life measures per gene averaged across collected datasets, and PCA is performed on the gene x… See the full description on the dataset page: https://huggingface.co/datasets/morrislab/rnahl-saluki-human.rna-stability-siegel
Overview
This dataset contains 3' UTR fragment measurements from the fast-UTR
massively parallel reporter assay reported by Siegel et al. The source library
contains 41,255 sequences tested in Jurkat T cells and BEAS-2B airway
epithelial cells. Each configuration retains rows with a T4 stability target,
a T4 effect target, or a reference needed to pair a measured effect. The
library contains native human 3' UTR fragments, natural variants, and designed
mutations of regulatory… See the full description on the dataset page: https://huggingface.co/datasets/morrislab/rna-stability-siegel.rnastralign
RNAStrAlign
RNAStrAlign is a comprehensive dataset of RNA sequences and their secondary structures.
RNAStrAlign aggregates data from multiple established RNA structure repositories, covering diverse RNA families such as 5S ribosomal RNA, tRNA, and group I introns.
It is considered complementary to the ArchiveII dataset.
Disclaimer
This is an UNOFFICIAL release of the RNAStrAlign by Zhen Tan, et al.
The team releasing RNAStrAlign did not write this dataset card for… See the full description on the dataset page: https://huggingface.co/datasets/multimolecule/rnastralign.rna-loc-fazal
Overview
mRNA localization annotates the subcellular compartments that mRNA are found in. This task is a multilabel classification -- mRNA can be found in more than one compartment. This dataset was computed from experimental APEX RNA seq data collected by Fazal et al. 2019.
This dataset is redistributed as part of mRNABench: https://github.com/morrislab/mRNABench
Data Format
Description of data columns:
target: Multihot labelling of cellular components that an mRNA… See the full description on the dataset page: https://huggingface.co/datasets/morrislab/rna-loc-fazal.operon-identification-long-read-rna-sequencing-protein-sequences
Dataset for operon identification from long-read RNA sequencing
A dataset of annotated operons across 5 distinct bacterial strains. The operons were annotated by running and analysing long-read RNA sequencing and identifying genes
located on the same transcripts.
The genome protein sequences have been extracted from GenBank. Each row contains whole bacterial genome represented by an ordered list
of protein sequences.
Usage
For a complete example on how to read and use… See the full description on the dataset page: https://huggingface.co/datasets/macwiatrak/operon-identification-long-read-rna-sequencing-protein-sequences.gtex-single-cell-rnaseq
GTEx Single-Cell RNA-seq Dataset
This repository provides tools to create a Hugging Face dataset from GTEx single-nucleus RNA-seq data, transforming the hierarchical H5AD format into a flat, ML-ready structure.
Overview
Data Source
The data comes from GTEx's snRNA-seq atlas:
Source: GTEx Portal
Publication: Eraslan et al., Science 2022 - "Single-nucleus cross-tissue molecular reference maps toward understanding disease gene function"
Content: 209… See the full description on the dataset page: https://huggingface.co/datasets/ai-department-lpnu/gtex-single-cell-rnaseq.rnahl-saluki-mouse
Overview
mRNA half-life is a measure of the degradation rate of mRNA molecules. This experiment reports the time that the expression level of a transcript takes to decrease by half. The original data source aggregates 39 human and 27 mouse transcriptome wide datasets -- this dataset contains the mouse datasets. Several data preprocessing steps are taken, reported in the original paper. Half-life measures per gene averaged across collected datasets, and PCA is performed on the gene x… See the full description on the dataset page: https://huggingface.co/datasets/morrislab/rnahl-saluki-mouse.rna-lifecycle-ietswaart
RNA Lifecycle Prediction
Overview
An mRNA molecule’s path from transcription to translation involves traversing multiple cellular compartments. This dataset, processed by mRNABench from experimental data by Ietswaart et al. (2024), provides an isoform-resolved map of this process using direct RNA sequencing.
The underlying assay captures RNA flow dynamics by measuring the rates at which transcripts are released from chromatin, exported from the nucleus, and loaded onto… See the full description on the dataset page: https://huggingface.co/datasets/morrislab/rna-lifecycle-ietswaart.litsumm-v1.5rnacentral.2048
RNAcentral
RNAcentral is a free, public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases representing a broad range of organisms and RNA types.
The development of RNAcentral is coordinated by European Bioinformatics Institute and is supported by Wellcome. Initial funding was provided by BBSRC.
Disclaimer
This is an UNOFFICIAL release of the RNAcentral by The… See the full description on the dataset page: https://huggingface.co/datasets/multimolecule/rnacentral.2048.Bulk-RNA-Seq-BenchmarkBulk RNA-seq benchmark for foundation-model evaluation: 58 tasks
(25 regression, 33 classification) across 38 datasets spanning
clinical outcome prediction, diagnostics, and biological/pharmacological phenotyping.
Format
One Parquet file per dataset in data/. Each row is a sample; columns are:
sample_id — sample accession (GSM / cell line / donor id).
gene columns — the native expression matrix X (gene-symbol headers).
y__<task> — one label column per task on that dataset. NaN… See the full description on the dataset page: https://huggingface.co/datasets/mibohl/Bulk-RNA-Seq-Benchmark.litsumm-v1RNAembedding_multiRNArelease-27
RNAcentral Release 27
This is an official HuggingFace version of the RNAcentral Release 27 available at https://rnacentral.org/
Included in this dataset are:
Unique ncRNA sequences for 46,210,324 sequences from our member databases.
Using the data
All RNAcentral data is provided with a CC-0 license, so you are free to do as you with with it.
If you do make use of our data, please consider citing our paper: https://doi.org/10.1093/nar/gkaf1329… See the full description on the dataset page: https://huggingface.co/datasets/RNAcentral/release-27.rnacentral.4096
RNAcentral
RNAcentral is a free, public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases representing a broad range of organisms and RNA types.
The development of RNAcentral is coordinated by European Bioinformatics Institute and is supported by Wellcome. Initial funding was provided by BBSRC.
Disclaimer
This is an UNOFFICIAL release of the RNAcentral by The… See the full description on the dataset page: https://huggingface.co/datasets/multimolecule/rnacentral.4096.bioreason_rnarnacentral.1024
RNAcentral
RNAcentral is a free, public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases representing a broad range of organisms and RNA types.
The development of RNAcentral is coordinated by European Bioinformatics Institute and is supported by Wellcome. Initial funding was provided by BBSRC.
Disclaimer
This is an UNOFFICIAL release of the RNAcentral by The… See the full description on the dataset page: https://huggingface.co/datasets/multimolecule/rnacentral.1024.Different_RNA_Typesrnacentral.8192
RNAcentral
RNAcentral is a free, public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases representing a broad range of organisms and RNA types.
The development of RNAcentral is coordinated by European Bioinformatics Institute and is supported by Wellcome. Initial funding was provided by BBSRC.
Disclaimer
This is an UNOFFICIAL release of the RNAcentral by The… See the full description on the dataset page: https://huggingface.co/datasets/multimolecule/rnacentral.8192.rna-lifecycle-ietswaart
RNA Lifecycle Prediction
Overview
An mRNA molecule’s path from transcription to translation involves traversing multiple cellular compartments. This dataset, processed from experimental data by Ietswaart et al. (2024), provides an isoform-resolved map of this process using direct RNA sequencing.
The underlying assay captures RNA flow dynamics by measuring the rates at which transcripts are released from chromatin, exported from the nucleus, and loaded onto polysomes for… See the full description on the dataset page: https://huggingface.co/datasets/anonymous-flamingo/rna-lifecycle-ietswaart.beacon-noncoding-rna-family
BEACON — NoncodingRNAFamily
Non-coding RNA family classification data.
Official data from the shared BEACON/RNABenchmark Drive folder:
https://drive.google.com/drive/folders/19ddrwI8ycvIxkgSV3gDo_VunLofYd4-6?hl=en.
This repository is the standardized Hugging Face publication of the official
task data. The data/ directory is the canonical viewer-friendly layer, and
the original files and directory layout are preserved for reproducibility.
beacon_manifest.json records source file… See the full description on the dataset page: https://huggingface.co/datasets/jiahaozhang2003/beacon-noncoding-rna-family.