Browse published AI skills maintained by BIsnake2001. Compare skill descriptions and follow each source repository for setup instructions.
Indexed skills
33Repository stars across indexed skills
99Repository forks
66Average repository stars per indexed skill
3Repository stars may repeat across skills from the same repository.
This skill should be used when users need to infer chromatin states from histone modification ChIP-seq data using chromHMM. It provides workflows for chromatin state segmentation, model training, state annotati...
Perform GO and KEGG functional enrichment using HOMER from genomic regions (BED/narrowPeak/broadPeak) or gene lists, and produce R-based barplot/dotplot visualizations. Use this skill when you want to perform G...
This skill identifies the locations of known transcription factor (TF) binding motifs within genomic regions such as ChIP-seq or ATAC-seq peaks. It utilizes HOMER to search for specific sequence motifs defined...
This skill analyzes the local DNA methylation profiles around target genomic regions provide by user. Use this skill when you want to vasulize the average methylation profile around target regions (e.g. TSS, CT...
Automatically detect and normalize Hi-C data. Only .cool or .mcool file is supported. All .mcool files are then checked for existing normalization (supports bins/weight only) and balanced if none of the normali...
This skill is used to perform genomic feature annotation and visualization for any file containing genomic region information using Homer (Hypergeometric Optimization of Motif EnRichment). It annotates regions...
Performs data cleaning and removal operations. This skill takes a raw BAM and creates a new, "clean" BAM file by actively removing artifacts: mitochondrial reads, blacklisted regions, PCR duplicates, and unmapp...
This skill annotates chromatin loops, including enhancer/promoter assignments, CTCF-peak overlap. It automatically constructs enhancer and promoter sets when missing and outputs standardized loop categories.
Calculates technical mapping statistics for any aligned BAM file (ChIP or ATAC). It assesses the performance of the aligner itself by generating metrics on read depth, mapping quality, error rates, and read gro...
This skill detects hierarchical (nested) TAD structures from Hi-C contact maps (in .cool or mcool format) using OnTAD, starting from multi-resolution .mcool files. It extracts a user-specified chromosome and re...
Perform peak calling for ChIP-seq or ATAC-seq data using MACS3, with intelligent parameter detection from user feedback. Use it when you want to call peaks for ChIP-seq data or ATAC-seq data.
This skill performs PCA-based A/B compartments calling on Hi-C .mcool datasets using pre-defined MCP tools from the cooler-tools, cooltools-tools, and plot-hic-tools servers.
Performs ATAC-specific biological validation. It calculates metrics unique to chromatin accessibility assays, such as TSS enrichment scores and fragment size distributions (nucleosome banding patterns). Use thi...
This skill provides a complete and streamlined workflow for performing methylation variability and epigenetic heterogeneity analysis from whole-genome bisulfite sequencing (WGBS) data. It is designed for resear...
This skill should be used when users need to perform known motif enrichment analysis on ChIP-seq, ATAC-seq, or other genomic peak files using HOMER (Hypergeometric Optimization of Motif EnRichment). It identifi...
Performs ChIP-specific biological validation. It calculates metrics unique to protein-binding assays, such as Cross-correlation (NSC/RSC) and FRiP. Use this when you have filtered the BAM file and called peaks...
This skill manages experimental reproducibility, pooling, and consensus strategies. This skill operates in two distinct modes based on the input state. (1) Pre-Peak Calling (BAM Mode): It merges all BAMs, gener...
This skill performs differential topologically associating domain (TAD) analysis using HiCExplorer's hicDifferentialTAD tool. It compares Hi-C contact matrices between two conditions based on existing TAD defin...
This skill performs correlation analysis between differential methylation and differential gene expression, identifying genes with coordinated epigenetic regulation. It provides preprocessing and integration wo...
This skill performs chromatin loop detection from Hi-C .mcool files using cooltools.
This skill performs protein-mediated regulatory community analysis from ChIA-PET datasets and provide a way for visualizing the communities. Use this skill when you have a annotated peak file (in BED format) fr...
This skill performs genome-wide DNA methylation profiling. It supports single-sample and multi-sample workflows to compute methylation density distributions, genomic feature distribution of the methylation prof...
This skill performs differential DNA methylation analysis (DMRs and DMCs) between experimental conditions using WGBS methylation tracks (BED/BedGraph). It standardizes input files into per-sample four-column Me...
This skill should be used when users need to identify topologically associating domains (TADs) from Hi-C data in .mcools (or .cool) files or when users want to visualize the TAD in target genome loci. It provid...
The default order uses GitHub repository stars from our indexed data. Stars belong to the source repository and may be shared by multiple skills. They indicate repository interest, not skill installs or an independent quality score.