datasets
Training and evaluation data, with the modality, task and licence stated up front. Listed live from the Hugging Face Hub.
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_ribonanzaRNA_degradationBulk-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.RNAembedding_multiRNADifferent_RNA_TypesRNA-seq-gene-expressionLLM_Classifier_Dataset_2000athaliana_rnaseq_splicing
Arabidopsis thaliana RNA-seq Splicing Dataset
Dataset Description
This dataset contains splice junction information from Arabidopsis thaliana RNA-seq data across multiple tissues (shoot, root, leaf, flower).
Data Processing
RNA-seq data mapped to the reference genome using STAR
Splice junctions filtered based on supporting read counts
Junctions with ±2bp shifts merged using bedtools
Data split by chromosomes: chr 1-3 for training, chr 4 for validation, and chr… See the full description on the dataset page: https://huggingface.co/datasets/suzuki-2001/athaliana_rnaseq_splicing.sma-gse108094-motor-neuron-rnaseq
GSE108094 SMA Motor-Neuron RNA-seq
This repository contains processed RNA-sequencing results and GEO/SRA metadata for human SMA and control iPSC-derived motor neurons.
The experiment has eight libraries from four biological cell lines: two SMA and two control lines, each with two sequencing replicates. The repository contains the differential-expression output, alternative-splicing output, series matrix, MINiML family file, SOFT family file, and SRA run inventory. The… See the full description on the dataset page: https://huggingface.co/datasets/YannisTevissen/sma-gse108094-motor-neuron-rnaseq.NF-ToN-IoT-Attack_detailsbulk-rna-immuno-inflammation-cohorts
Datasets Included
5 disease-specific bulk RNA-seq datasets, each containing 200 samples aggregated from public GEO repositories.
obs (samples / observations)
Each row is one bulk RNA-seq sample with 4 metadata columns:
Column
Description
tissue
Biological tissue from which RNA was extracted
disease
Disease condition of the sample
sample_id
Individual GEO sample identifier (GSM...)
dataset_name
GEO series the sample belongs to (GSE...)… See the full description on the dataset page: https://huggingface.co/datasets/ScientaLab/bulk-rna-immuno-inflammation-cohorts.LLM_Classifier_Dataset_4000dpo_datasetRNA_LLPS_dataSRA_metadata_RNAseq_special_sets
RNA-seq Subsets Derived from the 1M Human SRA Metadata Dataset
Extracted from the 1M annotated sample: chumphati/1M_RNAseq_SRA_samples_annotations.
Annotated with Metappuccino (Fiona Hak, Camille Marchet, Daniel Gautheret, Mélina Gallopin, Metappuccino: large language model-driven reconstruction of sequence read archive metadata for cancer research, Bioinformatics, Volume 42, Issue 5, May 2026, btag166, https://doi.org/10.1093/bioinformatics/btag166).
CCLE-like… See the full description on the dataset page: https://huggingface.co/datasets/chumphati/SRA_metadata_RNAseq_special_sets.NF-ToN-IoT-Metadata_detailsphi3-4000-datasetNF-ToN-IoT-benignPaul_RNA_Sequence_Processed_DatasetLLM_Classifier_DatasetIoV-Metadata_detailsfalcon-4000-datasetPaul_RNA_Sequence_Unprocessed_DataNetwork_Corpuslitscan-abstracts
RNAcentral Litscan ncRNA Related Abstracts
This is a dataset of abstracts that have been labelled relevant to ncRNA or not. Relevant articles have the label 1, irrelevant have the label 0
How was it made
The dataset was built in five parts:
ncRNA related articles from tarbase
ncRNA related articles from Rfam
ncRNA related articles from GO curation
Manually annotated ncRNA related articles
Non ncRNA related articles
TarBase
TarBase is a database of miRNAs and… See the full description on the dataset page: https://huggingface.co/datasets/RNAcentral/litscan-abstracts.RNABANDtest01asrs