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Reusable instructions for compatible AI agents.
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Align short reads using Bowtie2 with local or end-to-end modes. Supports gapped alignment. Use when aligning ChIP-seq, ATAC-seq, or when flexible alignment modes are needed.
End-to-end metagenomics workflow from FASTQ to taxonomic and functional profiles. Covers Kraken2 classification, Bracken abundance estimation, and HUMAnN functional profiling. Use when profiling metagenomic samples.
Sequence QC, alignment, and BAM processing. Wraps FastQC, BWA/Bowtie2, SAMtools for automated read-to-BAM pipelines.
Aligns bisulfite-converted (WGBS, RRBS, PBAT) and enzymatic (EM-seq) short reads to an in-silico C->T/G->A-converted reference with Bismark (Bowtie2 or HISAT2), preparing the genome index, choosing the directional vs non-directional vs PBAT strand flag, deduplicating WGBS/EM-seq (never RRBS), and...
Preprocess ribosome profiling data including adapter trimming, size selection, rRNA removal, and alignment. Use when preparing Ribo-seq reads for downstream analysis of translation.
End-to-end Ribo-seq analysis from FASTQ to translation efficiency and ORF detection. Use when analyzing ribosome profiling data to study translation.
Align preprocessed CLIP-seq reads (eCLIP, iCLIP, iCLIP2, PAR-CLIP) to genome with STAR or bowtie2 using crosslink-preserving parameters, choosing between unique-mapper-only and multi-mapper-aware alignment for repeat-binding RBPs, deciding STAR vs HISAT2 memory trade-offs, and applying ENCODE-com...
Analyzes CUT&RUN (Skene Henikoff 2017) and CUT&Tag (Kaya-Okur 2019) chromatin profiling data. Handles SEACR vs MACS2 peak calling (with the btaf375 2025 benchmark guidance), pA-MNase vs pA-Tn5 vs pAG-Tn5 chimera differences, E. coli spike-in carryover normalization, IgG-only control logic (no inp...
Agent skill for Data Scientist, ML / AI Engineer, Researcher, published by diegosouzapw. Project details and file access are provided by the publisher.
Agent skill for Data Scientist, ML / AI Engineer, Researcher, published by BioTender-max. Project details and file access are provided by the publisher.
Agent skill for Data Scientist, ML / AI Engineer, Researcher, published by Rudson-Oliveira. Project details and file access are provided by the publisher.
Agent skill for Data Scientist, ML / AI Engineer, Researcher, published by FridrichMethod. Project details and file access are provided by the publisher.
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