Compute coverage, cis/trans ratios, and P(s) curves for Hi-C files.
npx skills add https://github.com/BIsnake2001/ChromSkills --skill hic-matrix-qc
Please help me install this Agent Skill. Skill: hic-matrix-qc Source: https://github.com/BIsnake2001/ChromSkills/tree/main/30_toolBased.hic-matrix-qc Command: npx skills add https://github.com/BIsnake2001/ChromSkills --skill hic-matrix-qc
This QC skill assesses Hi-C data quality by computing coverage, cis/trans ratios, and distance-dependent contact decay (P(s)) for .cool, .mcool, or .hic inputs, enabling reliable downstream analyses.
Run hic-matrix-qc on your Hi-C files to generate QC metrics and plots for your chosen resolution.
High-intent search queries and answers about installing and using this skill.
Run Hi-C matrix QC by providing a .cool, .mcool, or .hic file path, a genome assembly, and a chosen resolution. It uses cooler and cooltools to compute per-bin coverage, cis/trans ratios, and outputs metrics with plots in a structured directory.
Distance-dependent contact decay P(s) measures how Hi-C contact frequency decreases as genomic distance increases. This skill generates P(s) curves and decay plots to evaluate contact frequency as a function of genomic distance for your input matrix.
Yes, you can compare Hi-C replicates at a user-selected resolution. The skill computes correlation metrics across multiple replicate files to identify inconsistencies, assess experimental reproducibility, and outputs a replicates-comparison report.
Yes, the Hi-C QC workflow supports .cool, .mcool, and .hic file formats as inputs. You provide the file path along with the genome assembly and chosen resolution to generate per-bin metrics, plots, and a QC summary.
You need to provide a Hi-C file path, a genome assembly, and a chosen resolution. The skill applies cooler and cooltools to generate per-bin metrics, decay plots, and a structured QC directory with logs and a replicates-comparison report.
Assessing Hi-C data quality ensures reliability for downstream analyses by computing coverage, cis/trans ratios, and P(s) decay. This QC identifies replicate inconsistencies and generates metrics with plots to guide subsequent genome analysis steps.
BIsnake2001Identify TAD boundaries from Hi-C data and visualize them on specified genomic regions.
fmschulzCluster proteins from FASTAs into pan-genome presence/absence matrices using MMseqs2 or ProteinOrtho.
BIsnake2001Detect chromatin loops from Hi-C data using cooltools and output BEDPE files.
danilomongeProcess Hi-C sequencing data into standardized analysis outputs.
