Agent Skills by yuxuanzhang
Showing 33 vetted skills indexed across 1 GitHub repositories.
BIsnake2001hic-compartments-calling
Call A/B compartments from Hi-C contact maps using PCA-based PC1 scoring.
BIsnake2001known-motif-enrichment
Identify known transcription factor motif enrichments in genomic peak regions using HOMER.
BIsnake2001functional-enrichment
Run GO and KEGG enrichment from genomic regions or gene lists with HOMER and R plots.
BIsnake2001regulatory-community-analysis-ChIA-PET
Build peak-centered chromatin interaction networks from ChIA-PET BEDPE and BED files.
BIsnake2001differential-tad-analysis
Identify differential TADs by comparing normalized Hi-C matrices with HiCExplorer.
BIsnake2001correlation-methylation-epiFeatures
Integrate CpG methylation BED data with chromatin bigWig signals to generate region_signal_table.tsv and correlation matrices.
BIsnake2001ATACseq-QC
Compute TSS enrichment, fragment-size distributions, and FRiP from BAM and peak files.
BIsnake2001genomic-feature-annotation
Annotate genomic regions with gene-based features using Homer or ChIPseeker.
BIsnake2001De-novo-motif-discovery
Identify enriched transcription factor motifs in genomic regions using HOMER.
BIsnake2001differential-region-analysis
Identify condition-dependent genomic regions from count data using DESeq2.
BIsnake2001methylation-variability-analysis
Identify CpG-level methylation variability across WGBS samples using R workflows.
BIsnake2001track-generation
Convert filtered BAM files into RPM-normalized BigWig tracks.
BIsnake2001TF-differential-binding
Identify differentially bound transcription factor regions from ChIP-seq data using DiffBind.
BIsnake2001peak-calling
Automate peak calling from BAM files for ChIP-seq and ATAC-seq experiments.
BIsnake2001loop-annotation
Annotate chromatin loops with regulatory features from bedpe inputs using HOMER.
BIsnake2001BAM-filtration
Remove mitochondrial reads, blacklist regions, PCR duplicates, and unmapped reads from coordinate-sorted BAMs.
BIsnake2001chromatin-state-inference
Infer chromatin states from histone modification ChIP-seq data using ChromHMM.
BIsnake2001atac-footprinting
Identify transcription factor occupancy from ATAC-seq footprints using TOBIAS.
BIsnake2001ChIPseq-QC
Compute NSC/RSC cross-correlation and FRiP metrics from aligned BAMs and peak files.
BIsnake2001alignment-level-QC
Calculate alignment-level QC metrics for ChIP-seq and ATAC-seq BAM files.
BIsnake2001hic-compartment-shift
Analyze Hi-C PC1 eigenvectors to identify A/B compartment shifts between conditions.
BIsnake2001differential-methylation
Identify differential DNA methylation regions and sites from WGBS BED/BedGraph inputs.
BIsnake2001replicates-incorporation
Merges BAMs and generates pseudo-replicates for reproducible peak analysis.
BIsnake2001hic-matrix-qc
Compute coverage, cis/trans ratios, and P(s) curves for Hi-C files.