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.
1---2name: upstream-processing-skills-index3description: 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.4---5
6# Upstream Processing Skills
7
8Skills and workflows for upstream data processing steps that precede
9standard single-cell analysis (QC, normalization, clustering, etc.).
10These cover technology-specific pipelines from raw sequencing data
11to analysis-ready count matrices with spatial coordinates.
12
13## Available Skills
14
15### OpenST
16
17Open-ST is an open-source spatial transcriptomics technology that captures
18transcriptome-wide data at sub-cellular resolution. The computational pipeline
19covers flow cell barcode preprocessing, transcriptomic alignment via spacemake,
20image-to-coordinate registration, cell segmentation, and 3D reconstruction.
21
22**Skill directory**: [openst/](./openst/)
23
24**When to use**:
25- Processing raw Open-ST data from BCL files to spatially-resolved h5ad
26- Aligning transcriptomic coordinates to H&E tissue images
27- Cell segmentation and transcript-to-cell assignment
28- 3D reconstruction from serial tissue sections
29
30---
31
32### nf-core Pipelines
33
34nf-core is a community-driven collection of 143+ curated Nextflow pipelines for
35bioinformatics. Skills cover installation, configuration, and pipeline-specific
36guides for transcriptomics, spatial omics, epigenomics, and variant calling.
37
38**Skill directory**: [nfcore/](./nfcore/)
39
40**When to use**:
41- Processing scRNA-seq data (10x, Drop-seq, Smart-seq) with nf-core/scrnaseq
42- Processing spatial transcriptomics (Visium, Xenium, MERSCOPE) with nf-core pipelines
43- Processing bulk RNA-seq, ATAC-seq, ChIP-seq, CUT&Run, or methylation data
44- Variant calling from WGS/WES with nf-core/sarek
45- Setting up Nextflow and nf-core on HPC clusters or cloud environments
46
47---
48
49## Using Skills
50
511. **Identify your technology**: Find the relevant sub-directory for your spatial/sequencing platform
522. **Load skill files**: Read the full skill documents for step-by-step guidance
533. **Follow the pipeline**: Upstream processing is sequential; follow stages in order
544. **Proceed to downstream analysis**: After generating the count matrix, use the main omics skills for QC, clustering, etc.
gabrielmoreira