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Annotates ChIP-seq peaks to genomic features, nearest genes, ENCODE candidate cis-regulatory elements (cCREs), and regulatory domains. Uses ChIPseeker (R), HOMER annotatePeaks.pl (CLI), pyranges (Python), GREAT/rGREAT (regulatory domain gene-set enrichment), ChIP-Enrich (locus-length-adjusted), E...
De novo and known TF motif enrichment in ChIP-seq/ATAC-seq peaks via HOMER. findMotifsGenome.pl finds over-represented patterns vs background; annotatePeaks.pl assigns context (TSS distance, gene, repeat). Use after MACS3 to identify enriched TFs, annotate peaks with nearest genes, and validate C...
Identifies super-enhancers from H3K27ac, MED1, or BRD4 ChIP-seq using ROSE, ROSE2, LILY, HOMER -style super, and ENCODE dELS cross-referencing. Handles peak stitching parameters, ranking choices, hockey-stick inflection, marker choice (H3K27ac vs MED1/BRD4), and cross-condition comparison with sp...
Discovers de novo motifs and tests known motif enrichment in ChIP-seq, ATAC-seq, or other peak sequences using HOMER, MEME-ChIP (STREME, CentriMo, TOMTOM, FIMO), monaLisa, and AME. Handles background selection (GC-matched, dinucleotide-shuffled, Markov order-2, peak-flanks), motif databases (JASP...
Agent skill for Data Analyst, Business Intelligence Analyst, Researcher, published by majiayu000. Project details and file access are provided by the publisher.
Agent skill for Researcher, Data Scientist, Clinical Research, published by BioTender-max. Project details and file access are provided by the publisher.
Agent skill for Researcher, Data Scientist, Business Intelligence Analyst, published by BIsnake2001. Project details and file access are provided by the publisher.
Agent skill for Researcher, Data Scientist, Business Intelligence Analyst, published by BIsnake2001. Project details and file access are provided by the publisher.
Agent skill for Researcher, Data Scientist, Business Intelligence Analyst, published by BIsnake2001. Project details and file access are provided by the publisher.
Agent skill for Researcher, Data Scientist, Business Intelligence Analyst, published by BIsnake2001. Project details and file access are provided by the publisher.
Agent skill for Data Scientist, Business Intelligence Analyst, Researcher, published by BIsnake2001. Project details and file access are provided by the publisher.
Agent skill for Researcher, Data Scientist, Business Intelligence Analyst, published by BIsnake2001. Project details and file access are provided by the publisher.
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