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golden-dataset-curation
Quality criteria, workflows, and multi-agent analysis patterns for curating high-quality golden dataset entries
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tools scientific computing AI Skills
Discover tools scientific computing skills, compare source repositories and read the instructions for each workflow.
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researcher
Researches topics in-depth and generates comprehensive summaries and references. Use when trying to deeply understand a topic or use a new framework.
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functional-enrichment
Perform GO and KEGG functional enrichment using HOMER from genomic regions (BED/narrowPeak/broadPeak) or gene lists, and produce R-based barplot/dotplot visualizations. Use this skill when you want to perform G...
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motif-scanning
This skill identifies the locations of known transcription factor (TF) binding motifs within genomic regions such as ChIP-seq or ATAC-seq peaks. It utilizes HOMER to search for specific sequence motifs defined...
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local-methylation-profile
This skill analyzes the local DNA methylation profiles around target genomic regions provide by user. Use this skill when you want to vasulize the average methylation profile around target regions (e.g. TSS, CT...
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hic-normalization
Automatically detect and normalize Hi-C data. Only .cool or .mcool file is supported. All .mcool files are then checked for existing normalization (supports bins/weight only) and balanced if none of the normali...
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genomic-feature-annotation
This skill is used to perform genomic feature annotation and visualization for any file containing genomic region information using Homer (Hypergeometric Optimization of Motif EnRichment). It annotates regions...
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loop-annotation
This skill annotates chromatin loops, including enhancer/promoter assignments, CTCF-peak overlap. It automatically constructs enhancer and promoter sets when missing and outputs standardized loop categories.
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alignment-level-qc
Calculates technical mapping statistics for any aligned BAM file (ChIP or ATAC). It assesses the performance of the aligner itself by generating metrics on read depth, mapping quality, error rates, and read gro...
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nested-tad-detection
This skill detects hierarchical (nested) TAD structures from Hi-C contact maps (in .cool or mcool format) using OnTAD, starting from multi-resolution .mcool files. It extracts a user-specified chromosome and re...
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peak-calling
Perform peak calling for ChIP-seq or ATAC-seq data using MACS3, with intelligent parameter detection from user feedback. Use it when you want to call peaks for ChIP-seq data or ATAC-seq data.
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hic-compartments-calling
This skill performs PCA-based A/B compartments calling on Hi-C .mcool datasets using pre-defined MCP tools from the cooler-tools, cooltools-tools, and plot-hic-tools servers.
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atacseq-qc
Performs ATAC-specific biological validation. It calculates metrics unique to chromatin accessibility assays, such as TSS enrichment scores and fragment size distributions (nucleosome banding patterns). Use thi...
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known-motif-enrichment
This skill should be used when users need to perform known motif enrichment analysis on ChIP-seq, ATAC-seq, or other genomic peak files using HOMER (Hypergeometric Optimization of Motif EnRichment). It identifi...
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chipseq-qc
Performs ChIP-specific biological validation. It calculates metrics unique to protein-binding assays, such as Cross-correlation (NSC/RSC) and FRiP. Use this when you have filtered the BAM file and called peaks...
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replicates-incorporation
This skill manages experimental reproducibility, pooling, and consensus strategies. This skill operates in two distinct modes based on the input state. (1) Pre-Peak Calling (BAM Mode): It merges all BAMs, gener...
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hic-loop-calling
This skill performs chromatin loop detection from Hi-C .mcool files using cooltools.
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regulatory-community-analysis-chia-pet
This skill performs protein-mediated regulatory community analysis from ChIA-PET datasets and provide a way for visualizing the communities. Use this skill when you have a annotated peak file (in BED format) fr...
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global-methylation-profile
This skill performs genome-wide DNA methylation profiling. It supports single-sample and multi-sample workflows to compute methylation density distributions, genomic feature distribution of the methylation prof...
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differential-methylation
This skill performs differential DNA methylation analysis (DMRs and DMCs) between experimental conditions using WGBS methylation tracks (BED/BedGraph). It standardizes input files into per-sample four-column Me...
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hic-compartment-shift
This skill performs A/B compartment shift analysis between two Hi-C samples.
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track-generation
This skill generates normalized BigWig (.bw) tracks (and/or fold-change tracks) from BAM files for ATAC-seq and ChIP-seq visualization. It handles normalization (RPM or fold-change) and Tn5 offset correction au...
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gsdworkflowresearch
Workflow for conducting research
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python-scientific-computing
Python for engineering analysis, numerical computing, and scientific workflows using NumPy, SciPy, SymPy
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The default order uses GitHub repository stars from our indexed data. Stars belong to the source repository and may be shared by multiple skills. They indicate repository interest, not skill installs or an independent quality score.