Upstream Processing Skills Index
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- Author repo PantheonOS
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/
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 directory: nfcore/
When to use:
- Processing scRNA-seq data (10x, Drop-seq, Smart-seq) with nf-core/scrnaseq
- Processing spatial transcriptomics (Visium, Xenium, MERSCOPE) with nf-core pipelines
- Processing bulk RNA-seq, ATAC-seq, ChIP-seq, CUT&Run, or methylation data
- Variant calling from WGS/WES with nf-core/sarek
- Setting up Nextflow and nf-core on HPC clusters or cloud environments
Using Skills
- Identify your technology: Find the relevant sub-directory for your spatial/sequencing platform
- Load skill files: Read the full skill documents for step-by-step guidance
- Follow the pipeline: Upstream processing is sequential; follow stages in order
- Proceed to downstream analysis: After generating the count matrix, use the main omics skills for QC, clustering, etc.
- Fluxly category
- Engineering
- Author-declared agents
- No explicit declaration found; this is not inferred or tested compatibility
- Static check
- 88 / 100 · heuristic scan, not runtime safety proof
- Author / version / license
- @aristoteleo · no license declared
- Fluxly token estimate
- Lean
- Fluxly setup estimate
- Plug-and-play
- External API key
- No requirement detected
- Detected OS requirements
- Unspecified
- Runtime requirements
- Unspecified
- Detected file/system behavior
-
- Read-only
- Detected network behavior
- Local-only
- Install commands
- None (reference only)
Profile is derived at build time from SKILL.md and install vectors. Subject to drift from author intent.
Heads up: 未限定 allowed-tools，默认拥有全部工具权限。
The current SKILL.md does not define a fixed output example.Available Skills
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,
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.
Identify your technology: Find the relevant sub-directory for your spatial/sequencing platform Load skill files: Read the full skill documents for step-by-step guidance Follow the pipeline: Upstream processing is sequential; follow stages in order
# 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 directory**: [nfcore/](./nfcore/)
**When to use**:
- Processing scRNA-seq data (10x, Drop-seq, Smart-seq) with nf-core/scrnaseq
- Processing spatial transcriptomics (Visium, Xenium, MERSCOPE) with nf-core pipelines
- Processing bulk RNA-seq, ATAC-seq, ChIP-seq, CUT&Run, or methylation data
- Variant calling from WGS/WES with nf-core/sarek
- Setting up Nextflow and nf-core on HPC clusters or cloud environments
---
## Using Skills
1. **Identify your technology**: Find the relevant sub-directory for your spatial/sequencing platform
…Author text anchors workflow facts; Fluxly only indexes current sections, terms, files, and commands.
sections -> Available Skills → OpenST → nf-core Pipelines → Using Skills
terms -> Skill directory · When to use · Identify your technology · Load skill files · Follow the pipeline · Proceed to downstream analysis
files/cmd -> ./openst · ./nfcore · nf-core/scrnaseq · WGS/WES · nf-core/sarek · spatial/sequencing
body sha256 -> db9e5be1aea0
Decide Fit First
Design Intent
How To Use It
Boundaries And Review