Integrations & APIs

fridrichmethod Bundle

Integrates spatial RNA with a second modality (protein, ATAC, or histone marks) on spatial CITE-seq, DBiT-seq, spatial-ATAC, or Visium CytAssist data. Use when deciding vertical (same-pixel co-profiling -> WNN/MOFA joint factors) versus diagonal (serial adjacent sections -> registration via PASTE/STalign) integration; recognizing that modalities from serial sections are DIFFERENT cells so joint same-cell methods do not apply; handling a bounded antibody/feature panel where absence is uninformative; or treating a pixel/spot as a multi-cell mixture rather than a single cell.

fridrichmethod Bundle

Programmatic untargeted LC-MS feature extraction in R with the modern xcms 4.x MsExperiment/XcmsExperiment API, taking raw mzML to a feature table via CentWave peak detection, retention-time alignment, peak-density correspondence, gap-filling, CAMERA redundancy collapse, and built-in QC feature filtering. Use when converting centroided LC-MS runs into a features-by-samples matrix and deciding centWave/grouping/alignment parameters. For drift correction and QC/CV filtering execution see metabolomics/normalization-qc; for metabolite identification see metabolomics/metabolite-annotation; for the MS-DIAL GUI alternative with MS2Dec deconvolution see metabolomics/msdial-preprocessing; for downstream statistics see metabolomics/statistical-analysis.

fridrichmethod Skill

Cancer genomics (TCGA et al.) via cBioPortal REST API. Retrieve somatic mutations, CNAs, expression, clinical data (survival/stage/treatment) across thousands of studies. Use for TMB, oncoprints, survival analysis. For population frequencies use gnomad-database; for drug-gene interactions use opentargets-database.

fridrichmethod Bundle

How to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieval. Use this skill whenever the user mentions Adaptyv, Foundry API, protein binding assays, protein screening experiments, BLI/SPR assays, thermostability assays, or wants to submit protein sequences for experimental characterization. Also trigger when code imports `adaptyv`, `adaptyv_sdk`, or `FoundryClient`, or references `foundry-api-public.adaptyvbio.com`.

fridrichmethod Bundle

Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.

fridrichmethod Bundle

Hardware-agnostic quantum ML framework with automatic differentiation. Use when training quantum circuits via gradients, building hybrid quantum-classical models, or needing device portability across IBM/Google/Rigetti/IonQ. Best for variational algorithms (VQE, QAOA), quantum neural networks, and integration with PyTorch or JAX. For hardware-specific optimizations use qiskit (IBM) or cirq (Google); for open quantum systems use qutip.

fridrichmethod Bundle

Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython.

fridrichmethod Bundle

Orders and orients assembled contigs into chromosome-scale scaffolds from long-range linking data, inserting N-gap spacers (adds no sequence). Covers Hi-C/Omni-C scaffolding (YaHS, SALSA2, 3D-DNA/Juicer), Hi-C read-mapping prerequisites (map each end separately, no mate rescue, dedup, enzyme-aware), reading the contact map for misjoins/inversions/false-duplications, manual curation in Juicebox/PretextView (the VGP/DToL standard), reference-guided scaffolding (RagTag) and its karyotype-erasure hazard, genetic-map (ALLMAPS) and Bionano optical-map integration, chimera-breaking before scaffolding, gap-filling, and telomere/contig-vs-scaffold-N50 QC (tidk). Use when turning contigs into chromosomes with Hi-C, integrating a linkage map or optical map, choosing a scaffolder by available linking data, or judging whether a chromosome-scale assembly is trustworthy.

fridrichmethod Bundle

Produce and interpret PCA, t-SNE, UMAP, and PHATE plots for high-dimensional omics data with rigor about which method preserves what (variance, local structure, manifold, transitions), hyperparameter sensitivity, and the well-documented limits of 2D embeddings. Covers PCA biplot/scree/loadings, t-SNE PCA initialization (Kobak-Berens 2019), UMAP n_neighbors/min_dist trade-offs, and the Chari-Pachter 2023 critique. Use when visualizing high-dimensional data — bulk PCA, single-cell embeddings, multi-omics integration projections.

26zl Bundle

Identifying and exploiting Insecure Direct Object Reference vulnerabilities to access unauthorized resources by manipulating object identifiers in API requests and URLs.

26zl Bundle

Automate OSINT collection using SpiderFoot REST API and CLI for target profiling, module-based reconnaissance, and structured result analysis across 200+ data sources

26zl Bundle

Detect and prevent API enumeration attacks including BOLA and IDOR exploitation by monitoring sequential identifier access patterns and authorization failures.

26zl Bundle

Performs rapid malware triage and classification using YARA rules to match file patterns, strings, byte sequences, and structural characteristics against known malware families and suspicious indicators. Covers rule writing, scanning, and integration with analysis pipelines. Activates for requests involving YARA rule creation, malware classification, pattern matching, sample triage, or signature-based detection.

26zl Bundle

Analyze the NTFS Master File Table ($MFT) to recover metadata and content of deleted files by examining MFT record entries, $LogFile, $UsnJrnl, and MFT slack space using MFTECmd, analyzeMFT, and X-Ways Forensics.

26zl Bundle

Design and implement Privileged Access Workstations (PAWs) with device hardening, just-in-time access, and integration with CyberArk or BeyondTrust for secure administrative operations.

fridrichmethod Bundle

Build and operate reproducible genomics workloads on DNAnexus with the dx CLI, dxpy, apps/applets, native workflows, dxCompiler, and Nextflow. Use for DNAnexus data transfers, dxapp.json development, execution monitoring, workflow import, and project automation.

fridrichmethod Skill

Benchling R&D Python SDK: CRUD on registry entities (DNA, RNA, proteins, custom), inventory, ELN, workflow automation. Needs Benchling account and API key. Use biopython for local sequence analysis; pubchem for chemical DBs.

fridrichmethod Bundle

Assesses genetic health of populations for conservation with Ne estimation across time horizons (LDNe NeEstimator V2 option-file API + SNeP physical-linkage correction; recent trajectory via GONE/GONE2; deep history via Stairway Plot 2 / dadi / fastsimcoal2 / PSMC), F-statistics, runs of homozygosity binned by length class to date inbreeding, genetic-load decomposition (Bertorelle 2022 realized vs masked), the modern 100/1000 Ne rule (Frankham 2014), Ne/Nc 2-6 orders of magnitude in marine fish (Hauser & Carvalho 2008), tree-sequence forward simulations (SLiM 4 + pyslim + tskit), and the Sukumaran-Knowles caveat against MSC methods for management-unit definition. Use when estimating Ne by time horizon, detecting inbreeding via F_ROH, decomposing genetic load, justifying conservation thresholds, distinguishing ESU/MU/DPS, configuring NeEstimator V2, or correcting LDNe physical linkage.

26zl Bundle

Execute and test GraphQL depth limit attacks using deeply nested recursive queries to identify denial-of-service vulnerabilities in GraphQL APIs.

26zl Bundle

Implements full disk encryption using Microsoft BitLocker on Windows endpoints to protect data at rest from unauthorized access in case of device loss or theft. Use when deploying encryption for compliance requirements, securing mobile workstations, or implementing data protection controls across the enterprise. Activates for requests involving BitLocker encryption, disk encryption, TPM configuration, or data-at-rest protection.

26zl Bundle

AES (Advanced Encryption Standard) is a symmetric block cipher standardized by NIST (FIPS 197) used to protect classified and sensitive data. This skill covers implementing AES-256 encryption in GCM m

26zl Bundle

Implements API rate limiting and throttling controls using token bucket, sliding window, and fixed window algorithms to protect against brute force attacks, credential stuffing, resource exhaustion, and API abuse. The engineer configures per-user, per-IP, and per-endpoint rate limits using Redis-backed counters, API gateway plugins, or application middleware, and implements proper HTTP 429 responses with Retry-After headers. Activates for requests involving rate limiting implementation, API throttling setup, request quota management, or API abuse prevention.

26zl Bundle

Executes malware samples in Cuckoo Sandbox to observe runtime behavior including process creation, file system modifications, registry changes, network communications, and API calls. Generates comprehensive behavioral reports for malware classification and IOC extraction. Activates for requests involving dynamic malware analysis, sandbox detonation, behavioral analysis, or automated malware execution.

26zl Bundle

Examine file system slack space, MFT entries, USN journal, and alternate data streams to recover hidden data and reconstruct file activity on NTFS volumes.

paulasilvatech Bundle

Retrieve and display GitHub Copilot usage metrics for organizations and enterprises using the GitHub CLI, REST API, and bundled scripts. Use when the user asks about Copilot usage, adoption, active users, acceptance rates, suggestions, chat interactions, per-user breakdowns, organization metrics, enterprise metrics, or usage on a specific date.

paulasilvatech Skill

Install, configure, emit, process, route, and troubleshoot Backstage notifications and optional real-time signals. Use when handling user or group notifications, external emitters, email or Slack processors, scaffolder notifications, settings, topics, or delivery failures.

paulasilvatech Skill

Prepare, implement, validate, and document contributions to backstage/backstage or a close fork using targeted tests, exact root typechecking, formatting, linting, API reports, changesets, DCO, and Apache headers. Use when changing Backstage core packages, plugins, docs, or contributor workflows.

paulasilvatech Skill

Generate technology-agnostic project workflow analysis blueprints that document end-to-end application flows, files, classes, entry points, service layers, data access, error handling, async processing, sequence diagrams, testing patterns, and implementation templates. Use this skill when the user asks to list all files/classes in a workflow, document representative workflows, map an API-to-database flow, or create an implementation-ready workflow blueprint.

paulasilvatech Bundle

Retrieve and display GitHub Copilot usage metrics for organizations and enterprises using the GitHub CLI, REST API, and bundled scripts. Use when the user asks about Copilot usage, adoption, active users, acceptance rates, suggestions, chat interactions, per-user breakdowns, organization metrics, enterprise metrics, or usage on a specific date.

paulasilvatech Skill

Generate personalized status briefings from a configured Roundup profile and available data sources such as GitHub, email, Teams, Slack, and Google Workspace. Use when the user asks for a roundup, leadership briefing, team update, weekly status, audience-specific update, or draft in their communication style.

paulasilvatech Bundle

Close bugs and incidents with an auditable BUG RECEIPT that states VERIFIED, PARTIAL, or BLOCKED based on baseline, root cause, change, proof, gaps, and evidence source. Use when the user asks for defect repair, regression proof, production incident closeout, issue closure, machine-readable receipt JSON, or CI integration of bug evidence.

paulasilvatech Bundle

Use this skill when the user works with RHDH Jira projects RHIDP, RHDHPLAN, RHDHBUGS, or RHDHSUPP using acli, GraphQL, and REST fallback. Trigger for Jira keys, creating features, epics, stories, tasks, bugs, assigning owners, refinement, sprint planning, sprint reports, release status, status updates, duplicate checks, sizing, or sprint ceremony prep.

paulasilvatech Bundle

Run an end-to-end GitHub library release workflow with git and gh: inspect tags, classify public API changes, choose a SemVer bump, update CHANGELOG.md, create release/vX.Y.Z, push, and open a release PR. Use when asked to cut a release, bump a version, generate a changelog, create a release branch, or publish a new GitHub repository version.

26zl Bundle

Implement API abuse detection using token bucket, sliding window, and adaptive rate limiting algorithms to prevent DDoS, brute force, and credential stuffing attacks.

26zl Bundle

Conduct a thick client application penetration test to identify insecure local storage, hardcoded credentials, DLL hijacking, memory manipulation, and insecure API communication in desktop applications using dnSpy, Procmon, and Burp Suite.

26zl Bundle

Implements data loss prevention policies using Microsoft Purview to protect sensitive information across Exchange Online, SharePoint, OneDrive, Teams, endpoint devices, and Power BI. The analyst configures sensitivity labels with encryption and content marking, creates DLP policies using built-in and custom sensitive information types with regex patterns, deploys endpoint DLP rules to control file operations on Windows and macOS devices, and monitors policy effectiveness through Activity Explorer and DLP alert management. Uses PowerShell cmdlets and the Microsoft Graph API for programmatic policy management. Activates for requests involving DLP policy creation, sensitivity label configuration, data classification, endpoint data protection, or Microsoft Purview compliance administration.