Database Access Skills Index
Skills for querying and downloading data from genomic, transcriptomic, 3D-genome, and cancer-genomics databases. Covers programmatic access to public repositories, gene annotation, sequence retrieval, processed functional-genomics tracks, Hi-C / Micro-C contact matrices, TCGA-style cohorts, and large-scale single-cell data.
npx skills add BioTender-max/awesome-bio-agent-skills --skill database_access --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Database Access Skills Tools and workflows for accessing public biological databases, retrieving sequencing data, querying gene/protein information, pulling processed functional / 3D-genome tracks, fetching cancer-cohort data, and downloading large-scale single-cell datasets. ## Quick map — which skill for what | If you need... | Use | |---|---| | Gene / protein / variant **metadata** (Ensembl, UniProt, NCBI, …) | **gget** | | Raw sequencing **reads** (FASTQ) from SRA/ENA/GEO/DDBJ/GSA | **iSeq** | | Large-scale **single-cell** RNA-seq matrices | **CELLxGENE Census** | | Processed **functional-genomics tracks** (ChIP/ATAC/DNase/RNA-seq bigWig/BAM/peaks) | **ENCODE** | | **3D-genome** contact matrices (Hi-C / Micro-C / ChIA-PET .mcool / .hic) | **4DN** | | **liftOver**, UCSC tracks, sequence pulls, large genome catalog | **UCSC** | | **Cancer-cohort** RNA-seq counts, MAF mutations, CNV, methylation (TCGA / CPTAC) | **GDC** | The new four (ENCODE / 4DN / UCSC / GDC) are mostly orthogonal to the existing three — they cover *processed* tracks, *3D* genome data, *coordinate utilities*, and *cancer cohorts* that gget / iSeq / Census don't reach. ## Available Skills ### gget — Genomic Da
- Quick map — which skill for what
- Available Skills
- gget — Genomic Database Querying
- iSeq — Sequencing Data Download
- CZ CELLxGENE Census — Single-Cell RNA-seq Data Access
- ENCODE — Functional Genomics Tracks (ChIP/ATAC/DNase/RNA-seq)
- 4DN — 3D Genome Data (Hi-C, Micro-C, ChIA-PET)
- UCSC — Genome Browser API + liftOver
- GDC — NCI Genomic Data Commons (TCGA + friends)
- Using Skills
What does the Database Access Skills Index skill do?
Skills for querying and downloading data from genomic, transcriptomic, 3D-genome, and cancer-genomics databases. Covers programmatic access to public repositories, gene annotation, sequence retrieval, processed functional-genomics tracks, Hi-C / Micro-C contact matrices, TCGA-style cohorts, and large-scale single-cell data.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill database_access --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.