bio-workflows-multiome-pipeline

bio-workflows-multiome-pipeline is a Bioinformatics & life sciences skill for AI agents, published by GPTomics in the bioSkills repository on GitHub. Skillspace rates bio-workflows-multiome-pipeline C (73/100) and it passed the safety scan; the rating is based on static analysis only.

Orchestrates the end-to-end 10x Multiome (paired scRNA + scATAC) pipeline from Cell Ranger ARC output to a jointly-embedded, annotated object, chaining per-modality QC, AMULET fragment-based ATAC doublet detection, per-modality normalization (RNA SCT/PCA; ATAC TF-IDF/LSI), WNN (or MultiVI) integration, joint clustering, RNA-based annotation, and LinkPeaks peak-to-gene linking. Use when enforcing the shared cell-barcode intersection between modalities (cellranger-ARC not -atac), keeping per-modality QC/doublets before the joint embedding, dropping the depth-correlated LSI component, annotating identity from RNA (ATAC is regulatory state), treating peak-to-gene links as correlational hypotheses, or aggregating to pseudobulk for cross-condition DE. Hands mechanism to the single-cell and atac-seq component skills; not a re-teach of any single step.

Grade

C

Quality

73 / 100

Safety

Passed

GitHub stars

1,025

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