Development

Obtenir et gérer un access token pour l'API Merci Facteur (envoi de courrier papier, recommandé, recommandé électronique). Utiliser dès qu'un appel à l'API Merci Facteur doit être authentifié, ou quand apparaît une erreur de signature, de timestamp, de restriction d'IP ou un token expiré. Couvre le calcul HMAC-SHA256 de la secret key, getToken, la durée de vie du token jusqu'à 365 jours (timeLimit, force) et le stockage des identifiants.

Annuler un envoi de courrier papier déjà validé via l'API Merci Facteur (deleteEnvoi). Utiliser quand il s'agit d'annuler, supprimer, stopper, rappeler ou rembourser un courrier envoyé par erreur, d'implémenter une fenêtre d'annulation dans une application, ou de comprendre pourquoi une annulation n'a été que partielle. Couvre le contrat deleteEnvoi, l'irréversibilité de l'opération et les quatre issues possibles.

Create, update, classify, and archive Obsidian documentation documents following structured vault conventions and templates.

Use when creating, changing, or validating a Cordis composition for this harness — writing or editing an agent preset, adding or removing a plugin row, deciding whether something belongs to the host composition or to one session, checking whether a preset you authored actually mounts, or diagnosing a row that mounted but contributed nothing.

Create, modify, debug, or extend dynamic Cordis Plugins, including Host Services and Events, Client Slot and theme UI, Package-private Client-to-Host calls, dynamic Tools, version updates, approval failures, and runtime diagnostics. Use this Skill to route a user request to the correct platform and Inspect Provider, then define, run, repair, or roll back the Plugin.

NCPGR高性能计算集群软件使用注意事项与优化指南。聚焦各软件的坑点、加速技巧、资源节省建议与软件选型推荐。当用户询问集群上如何高效使用软件、编写LSF作业、或需要软件选型建议时使用。

Use when users need bioinformatics analysis on the NCPGR cluster, especially when converting analysis requests into local software choices, resource plans, and LSF job scripts.

自动寻找当前网络环境下最快的 GitHub 代理镜像，用于克隆仓库、下载文件或获取 Release 资产。当需要从 github.com 下载任何内容时使用本 skill——包括 git clone、wget/curl 下载、Release 资产获取等。

Cell-free DNA analysis pipeline from plasma sequencing to tumor monitoring. Preprocesses cfDNA reads, analyzes fragment patterns, estimates tumor fraction from sWGS, and optionally detects mutations from targeted panels. Use when analyzing liquid biopsy samples for cancer detection or monitoring.

Workflow from differential expression results to functional enrichment analysis. Covers GO, KEGG, Reactome enrichment with clusterProfiler and visualization. Use when taking DE results to pathway enrichment.

Create portable, standards-based bioinformatics pipelines with Common Workflow Language (CWL). Use when building workflows that need maximum portability across execution platforms, sharing pipelines with collaborators using different systems, or contributing to community workflow registries.

View, query, and understand VCF/BCF variant files using bcftools and cyvcf2. Use when inspecting variants, extracting specific fields, or understanding VCF format structure.

Comprehensive variant annotation using bcftools annotate/csq, VEP, SnpEff, and ANNOVAR. Add database annotations, predict functional consequences, and assess clinical significance with MANE transcript selection and pathogenicity scoring. Use when annotating variants with functional and clinical information.

Comprehensive variant filtering including GATK VQSR, hard filters, bcftools expressions, and quality metric interpretation for SNPs and indels. Use when filtering variants using GATK best practices.

Discovers periodic signals of unknown period in time-series omics data using Lomb-Scargle periodograms (scipy), autocorrelation, and wavelet time-frequency decomposition (pywt). Identifies dominant frequencies, handles irregularly sampled data, and detects transient periodicity. Use when searching for periodic patterns of unknown period length, analyzing cell cycle oscillations, or processing unevenly spaced time-series. Not for testing known 24-hour rhythms (see temporal-genomics/circadian-r...

Detects circadian and ultradian rhythms in time-series omics data using CosinorPy cosinor models, MetaCycle (JTK_CYCLE, ARSER), and RAIN non-parametric tests. Fits cosine models to estimate phase and amplitude, tests rhythmicity significance at pre-specified periods. Use when testing for 24-hour or other known-period oscillations in circadian, feeding-fasting, or light-dark cycle experiments. Not for unknown-period discovery (see temporal-genomics/periodicity-detection).

Analyze single-cell TCR and BCR data integrated with gene expression using scirpy. Use when working with 10x Genomics VDJ data alongside scRNA-seq or when integrating immune receptor information with cell state analysis.

Build genome-scale metabolic models from genome sequences using CarveMe and gapseq for automated reconstruction. Generate draft models ready for curation and analysis. Use when creating metabolic models for organisms without existing models.

Perform in silico gene knockout analysis and synthetic lethality screens using COBRApy single and double deletions. Predict essential genes and identify synthetic lethal pairs for drug target discovery. Use when identifying essential genes or finding synthetic lethal drug targets.

Perform flux balance analysis (FBA) and flux variability analysis (FVA) on genome-scale metabolic models using COBRApy. Predict growth rates, metabolic fluxes, and optimal resource utilization. Use when predicting metabolic phenotypes or optimizing flux distributions.

Navigate protein structure hierarchy using Biopython Bio.PDB SMCRA model. Use when accessing models, chains, residues, and atoms, iterating over structure levels, or extracting sequences from PDB files.

Modify protein structures using Biopython Bio.PDB. Use when transforming coordinates, removing atoms or residues, adding new entities, modifying B-factors and occupancies, or building structures programmatically.

Parse and write protein structure files using Biopython Bio.PDB. Use when reading PDB, mmCIF, and MMTF files, downloading structures from RCSB PDB, or writing structures to various formats.

Perform geometric calculations on protein structures using Biopython Bio.PDB. Use when measuring distances, angles, and dihedrals, superimposing structures, calculating RMSD, or computing solvent accessible surface area (SASA).