GitHub
hic-loop-calling
This skill performs chromatin loop detection from Hi-C .mcool files using cooltools.
Skills IA Développement
Découvrez les skills Développement, comparez leurs dépôts et consultez leurs instructions.
Catégories: Développement
Développement Effacer les filtres
Explorer
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...
GitHub
atac-footprinting
This skill performs transcription factor (TF) footprint analysis using TOBIAS on ATAC-seq data. It corrects Tn5 sequence bias, quantifies TF occupancy at motif sites, generates footprint scores, and optionally...
GitHub
tf-differential-binding
The TF-differential-binding pipeline performs differential transcription factor (TF) binding analysis from ChIP-seq datasets (TF peaks) using the DiffBind package in R. It identifies genomic regions where TF bi...
GitHub
umr-lmr-pmd-detection
This pipeline performs genome-wide segmentation of CpG methylation profiles to identify Unmethylated Regions (UMRs), Low-Methylated Regions (LMRs), and Partially Methylated Domains (PMDs) using whole-genome bis...
GitHub
jira-auth
Authenticate with Jira Cloud REST API using API tokens. Use when setting up Jira connections, validating credentials, or handling rate limiting.
GitHub
jira-issues
Create, read, update, and delete Jira issues. Use when managing Stories, Tasks, Bugs, or Epics - includes field updates and metadata.
GitHub
jira-transitions
Move Jira issues through workflow states. Use when transitioning issues (To Do, In Progress, Done) or setting resolutions.
GitHub
jira-project-management
Administer Jira projects. Use when creating/archiving projects, managing components, versions, roles, permissions, or project configuration.
GitHub
jira-agile
Manage Jira Agile boards and sprints. Use when listing boards, creating sprints, or moving issues to/from sprints.
GitHub
jira-projects
Manage Jira projects. Use when listing projects, getting project configuration, retrieving issue types, or managing components and versions.
GitHub
jira-search
Search Jira issues using JQL queries. Use when filtering issues by project, status, assignee, date, or building reports.
GitHub
jira-spaces
Manage Confluence spaces for project documentation. Create, list, and delete spaces with templates. Use when setting up project documentation structure or managing Confluence content areas.
GitHub
speck-help
Answer questions about Speck specs, plans, tasks, requirements, progress, architecture, user stories, feature status, and constitution. Interprets spec.md, plan.md, tasks.md files. Use when users ask about feat...
GitHub
pr-review
Review GitHub pull requests with VSCode integration. Use when the user asks to "review a PR", "review PRs", "check pull requests", or wants AI-assisted code review with clickable navigation and one-click commen...
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.