smithery/BIsnake2001

1

atac-footprinting This skill performs transcription factor (TF) footprint analysis using TOBIAS on ATAC-seq data. It corrects Tn5 seque…

smithery/BIsnake2001

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ChIPseq-QC Performs ChIP-specific biological validation.

smithery/BIsnake2001

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chromatin-state-inference This skill should be used when users need to infer chromatin states from histone modification ChIP-seq data using chr…

smithery/BIsnake2001

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correlation-methylation-epiFeatures This skill provides a complete pipeline for integrating CpG methylation data with chromatin features such as ATAC-seq…

smithery/BIsnake2001

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hic-compartment-shift This skill performs A/B compartment shift analysis between two Hi-C samples.

smithery/BIsnake2001

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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 c…

smithery/BIsnake2001

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hic-loop-calling This skill performs chromatin loop detection from Hi-C .mcool files using cooltools.

smithery/BIsnake2001

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hic-tad-calling This skill should be used when users need to identify topologically associating domains (TADs) from Hi-C data in .mco…

smithery/BIsnake2001

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integrative-DMR-DEG This skill performs correlation analysis between differential methylation and differential gene expression, identifyi…

smithery/BIsnake2001

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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 …

smithery/BIsnake2001

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motif-scanning This skill identifies the locations of known transcription factor (TF) binding motifs within genomic regions such as …

smithery/BIsnake2001

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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…

smithery/BIsnake2001

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peak-calling Perform peak calling for ChIP-seq or ATAC-seq data using MACS3, with intelligent parameter detection from user feedba…

smithery/BIsnake2001

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UMR-LMR-PMD-detection This pipeline performs genome-wide segmentation of CpG methylation profiles to identify Unmethylated Regions (UMRs), …

smithery/BIsnake2001

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