HolobiomicsLab/asb-skill-collections

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have raw ChIP-Seq and control BED files with potential PCR duplicates or unequal sequencing depths. Duplicate filtering is mandatory before estimating fragment length (predictd) or generating coverage pileups.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when when you are developing or contributing to a Python package (like cooltools) and need to test changes to utility functions, library integrations, or API implementations without reinstalling the package after each modification. Apply this when you must verify that a new function (e.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have computed eigenvector values from a prior eigscis calculation on a cooler Hi-C matrix and need to classify genomic regions into discrete A/B compartment categories before performing saddle analysis or computing compartment-level contact asymmetry metrics.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have raw Hi-C FASTQ files from a public repository (NCBI SRA, GEO, or ENCODE-deposited accession) and need to reproduce or validate Hi-C map generation following the ENCODE uniform processing standard, or you need to verify that your pipeline output conforms to reference format and.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when after cloning or installing a peak-calling or genomic analysis tool from a repository, before using it on production data.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when when developing or validating a DNA methylation array analysis pipeline using ChAMP, you need an independent ground-truth dataset to confirm that DMR detection is working correctly.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when after merging methylation call files into a unified methylBase object (covering all samples at common base positions), apply this skill to assess whether biological replicates cluster together, whether case/control or treatment groups separate as expected, and to identify potential sample.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have a backed AnnData object containing processed fragment data (stored in .obsm['fragmentpaired'] or .

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when after invoking pp.makefragmentfile to convert a coordinate-sorted BAM file (e.g., from 10X ATAC or standard alignment) into a compressed fragment file.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when when beginning ChIP-Seq analysis with single-end BED/SAM input and no prior knowledge of the library's fragment length.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have paired-end ChIP-Seq data (BEDPE format) and need to determine the empirical fragment length (insertion length) before peak calling. This is mandatory for paired-end ChIP-Seq workflows to ensure MACS3 correctly extends coverage tracks and calculates local bias.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when after filtering duplicate reads from ChIP-Seq data but before generating pileup coverage tracks.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have a SummarizedExperiment object containing peak counts from single-cell or bulk ATAC-seq/DNAse-seq data and need to prepare it for unbiased motif deviation analysis.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have raw Hi-C FASTQ files from a kilobase-resolution Hi-C experiment and need to produce a processed Hi-C contact map (.hic file) for visualization, loop calling, or chromatin structure analysis. This is the entry point for any Hi-C dataset that has not yet been aligned and normalized.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have filtered peak or chromatin accessibility counts and need to annotate each peak with the presence or absence of specific DNA sequence patterns—either predefined motifs (e.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you need to map computed per-bin metrics (insulation scores, boundary calls, contact frequencies) back to genomic coordinates for export to BED/GFF format, cross-reference with external annotations, or validate that computed features fall within expected genomic ranges.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when after you have identified a set of differentially methylated bases or regions (e.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have a pre-generated .hic contact map file and need to identify and annotate chromatin loops or topologically associating domains (TADs) at high resolution.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when after bias-correcting ATAC-seq cutsite signal (via ATACorrect) when you have a bias-corrected bigWig file and need to compute per-position footprint scores within defined accessible regions (peaks, called footprints, or regulatory regions) to detect and quantify transcription factor.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have a cooler file (.cool or .mcool) from a Hi-C experiment and need to generate a genome-wide track of per-bin sequencing depth to assess coverage uniformity, identify poorly sequenced regions, or normalize downstream analyses by local sequencing intensity.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have a cooler-format Hi-C contact matrix and need to establish a genome-wide baseline contact frequency by genomic distance.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have raw Hi-C FASTQ files from a Hi-C wet-lab protocol and need to convert them into processed Hi-C contact maps (.hic files) for loop detection, TAD identification, or 3D structure inference. Use when starting from deposited public Hi-C datasets (e.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have raw Hi-C FASTQ files from a sequencing experiment and need to generate kilobase-resolution Hi-C contact maps conforming to ENCODE reference standards.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have a cooler-format Hi-C contact matrix and need to identify TAD boundaries and insulation strength along the genome. Use this skill when your research question requires quantifying local chromatin compartmentalization or annotating structural domain edges for downstream analysis (e.