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bam-filtration
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...
Skills IA Tests et sécurité
Découvrez les skills Tests et sécurité, comparez leurs dépôts et consultez leurs instructions.
Catégories: Tests et sécurité
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Explorer
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loop-annotation
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.
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alignment-level-qc
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...
GitHub
nested-tad-detection
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...
GitHub
peak-calling
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.
GitHub
hic-compartments-calling
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.
GitHub
atacseq-qc
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...
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methylation-variability-analysis
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...
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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 genomic peak files using HOMER (Hypergeometric Optimization of Motif EnRichment). It identifi...
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chipseq-qc
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...
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replicates-incorporation
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...
GitHub
differential-tad-analysis
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...
GitHub
integrative-dmr-deg
This skill performs correlation analysis between differential methylation and differential gene expression, identifying genes with coordinated epigenetic regulation. It provides preprocessing and integration wo...
GitHub
hic-loop-calling
This skill performs chromatin loop detection from Hi-C .mcool files using cooltools.
GitHub
regulatory-community-analysis-chia-pet
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...
GitHub
global-methylation-profile
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...
GitHub
differential-methylation
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...
GitHub
hic-tad-calling
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...
GitHub
hic-matrix-qc
This skill performs standardized quality control (QC) on Hi-C contact matrices stored in .mcool or .cool format. It computes coverage and cis/trans ratios, distance-dependent contact decay (P(s) curves), covera...
GitHub
correlation-methylation-epifeatures
This skill provides a complete pipeline for integrating CpG methylation data with chromatin features such as ATAC-seq signal, H3K27ac, H3K4me3, or other histone marks/TF signals.
GitHub
hic-compartment-shift
This skill performs A/B compartment shift analysis between two Hi-C samples.
GitHub
differential-region-analysis
The differential-region-analysis pipeline identifies genomic regions exhibiting significant differences in signal intensity between experimental conditions using a count-based framework and DESeq2. It supports...
GitHub
track-generation
This skill generates normalized BigWig (.bw) tracks (and/or fold-change tracks) from BAM files for ATAC-seq and ChIP-seq visualization. It handles normalization (RPM or fold-change) and Tn5 offset correction au...
GitHub
de-novo-motif-discovery
This skill identifies novel transcription factor binding motifs in the promoter regions of genes, or directly from genomic regions of interest such as ChIP-seq peaks, ATAC-seq accessible sites, or differentiall...
Le classement utilise les étoiles du dépôt GitHub indexé. Plusieurs skills peuvent partager ce nombre : ce n’est ni un nombre d’installations ni une note de qualité.