Upstream Processing Skills Index
Skills for upstream data processing in single-cell and spatial omics, covering raw data generation, barcode processing, alignment, spatial registration, and technology-specific preprocessing pipelines.
npx skills add BioTender-max/awesome-bio-agent-skills --skill upstream_processing --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.
# Upstream Processing Skills Skills and workflows for upstream data processing steps that precede standard single-cell analysis (QC, normalization, clustering, etc.). These cover technology-specific pipelines from raw sequencing data to analysis-ready count matrices with spatial coordinates. ## Available Skills ### OpenST Open-ST is an open-source spatial transcriptomics technology that captures transcriptome-wide data at sub-cellular resolution. The computational pipeline covers flow cell barcode preprocessing, transcriptomic alignment via spacemake, image-to-coordinate registration, cell segmentation, and 3D reconstruction. **Skill directory**: [openst/](./openst/) **When to use**: - Processing raw Open-ST data from BCL files to spatially-resolved h5ad - Aligning transcriptomic coordinates to H&E tissue images - Cell segmentation and transcript-to-cell assignment - 3D reconstruction from serial tissue sections --- ### nf-core Pipelines nf-core is a community-driven collection of 143+ curated Nextflow pipelines for bioinformatics. Skills cover installation, configuration, and pipeline-specific guides for transcriptomics, spatial omics, epigenomics, and variant calling. **Skill dir
- Available Skills
- OpenST
- nf-core Pipelines
- Using Skills
What does the Upstream Processing Skills Index skill do?
Skills for upstream data processing in single-cell and spatial omics, covering raw data generation, barcode processing, alignment, spatial registration, and technology-specific preprocessing pipelines.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill upstream_processing --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.