| --- |
| license: mit |
| task_categories: |
| - text-classification |
| - token-classification |
| - tabular-classification |
| - other |
| tags: |
| - bioinformatics |
| - genomics |
| - variant-calling |
| - machine-learning |
| - fantom5 |
| size_categories: |
| - 1G<n<2G |
| --- |
| |
| # Dataset Card for seqedge-data |
|
|
| ## Dataset Description |
|
|
| This repository serves as the official public data backend for **GalibierHub**, an interactive web platform for genomic cohort analytics. The dataset hosts reference bundles, release archives, and sample-level files designed for academic research and downstream bioinformatics pipelines. It currently contains approximately 1.3 GB of open-access data published under the MIT license. |
|
|
| ## Dataset Structure |
|
|
| The repository is organized into distinct directories to support both traditional bioinformatics workflows and machine learning applications. |
|
|
| **Core Academic Data (GalibierHub Records)** |
| * **Records/Reference_Genomes/**: Contains the global reference files, including `reference.fasta` and `annotation.gff3`. |
| * **Records/Variant_Calling_VCF/**: Contains 12 sample-specific `.vcf.gz` files tailored for variant and population genetics analysis. |
| * **Records/ML_Ready_FASTA/**: Contains 12 full `.fasta` files optimized for machine learning sequence extraction and promoter prediction. |
| |
| **Additional Resources** |
| * **SARS-CoV-2 Reference Files**: Root-level files including `scov2.fa`, `scov2.gb`, `scov2.genes.bed`, and `scov2.genes.gff3`. |
| * **Learning-Resources/**: A collection of educational materials and bioinformatics reference PDFs. |
| * **Graduate-student-textbooks/**: Supplemental textbooks for graduate-level study. |
| |
| ## Source Data Details |
| |
| The 12 primary demo samples located in the `Records/` directory (e.g., CNhs13076, CNhs13080, CNhs13195, CNhs13216) are derived from public test files. |
| * **Source**: FANTOM5 human primary-cell CAGE data (hg19) |
| * **Cohort**: FANTOM5 human.primary_cell.hCAGE |
| * **Platform**: HeliScope CAGE |
| * **Project URL**: https://fantom.gsc.riken.jp/5/ |
| * **Reference Publication**: https://www.nature.com/articles/sdata2017112 |
| |
| ## How to Use This Data |
| |
| Files can be downloaded directly from this repository using the Hugging Face CLI, `wget`, or `curl`. However, for the optimal experience, we recommend using the **GalibierHub Downloads Interface**, which provides: |
| * Automated generation of Python, SLURM, and `.bat` batch download scripts for recursive folder downloads. |
| * MD5 and SHA-256 integrity verification commands to ensure data is uncorrupted after transfer. |
| * Seamless routing from the embedded JBrowse 2 genome visualization directly to the corresponding file downloads. |
| |
| ## About GalibierHub |
| |
| GalibierHub is a comprehensive scientific data portal built for modern researchers. Key end-user capabilities include: |
| * **Search & Discovery**: Advanced filtering of promoter records by locus, gene, score, tissue, cohort, and BMI class. |
| * **Data Visualization**: An embedded genome browser with a distraction-free fullscreen zen mode and floating promoter detail panels. |
| * **Community & Moderation**: A rich discussion board featuring Markdown support, image lightboxes, real-time WebSocket notifications, and a gamified badge system to reward community contributions. |
| * **User Profiles**: Persistent profiles synced via Supabase with activity feeds, online status, and secure authentication (GitHub OAuth or Turnstile-protected email). |
| |
