Productivity

fridrichmethod Bundle

Filters reads by quality, length, N content, and complexity with Trimmomatic, fastp, and Cutadapt, including sliding-window trimming, per-read unqualified-base filtering, and 2-color poly-G removal. Use when reads have poor-quality tails, when an assembly or k-mer workflow needs clean input, or when a junk read subpopulation must be dropped. For adapter removal use adapter-trimming; for all-in-one preprocessing use fastp-workflow.

fridrichmethod Bundle

Import transcript-level quantifications from Salmon/kallisto/RSEM into R for gene-level analysis with DESeq2/edgeR using tximport or tximeta. Use when summarizing transcript abundances to gene counts with the correct length offset, choosing a countsFromAbundance mode (full-length vs 3'-tag vs DTU), resolving transcript-ID version mismatches, or handing off to DESeq2/edgeR without double-applying the offset.

fridrichmethod Bundle

Performs structure-based virtual screening using AutoDock Vina, SMINA, GNINA (CNN scoring), and DiffDock-L hybrid workflows with explicit choice rules across rigid vs flexible docking, cross-docking vs self-docking, binding-site detection (P2Rank, fpocket), receptor preparation (PDB2PQR, PROPKA), ligand preparation (meeko, OpenBabel), and ultralarge-library screening (ZINC22, Enamine REAL). Use when screening chemical libraries against a protein target to find candidate binders, ranking docking poses, or selecting a docking workflow for a specific scenario.

fridrichmethod Bundle

Identifies essential genes from CRISPR-Cas9 fitness screens using BAGEL2 (Kim & Hart 2021 Genome Med), a Bayesian classifier scoring per-gene Bayes Factors via log-likelihood ratios over per-sgRNA fold changes, calibrated against CEGv2 core-essentials (Hart 2017 G3, ~684 genes) and NEGv1 non-essentials (Hart 2014, ~927 genes). Covers the fc + bf + pr workflow, the linear-extrapolation improvement over BAGEL1 truncation, multi-target off-target correction, tumor-suppressor sensitivity (BAGEL2 detects enrichment), and BF calibration (BF >6 ≈ 90% posterior per Hart 2017; ~5% FDR by BAGEL convention). Use when classifying essential vs non-essential genes, calibrating BAGEL2 thresholds against PR curves, identifying tumor suppressors alongside essentials, comparing BAGEL2 hits to MAGeCK / drugZ, or generating publication-quality essentiality calls.

fridrichmethod Bundle

Infers ligand-receptor cell-cell communication from scRNA-seq with a consensus-first workflow (LIANA), plus CellPhoneDB specificity tests, CellChat pathway probabilities, and NicheNet downstream ligand-activity. Use when ranking ligand-receptor interactions between cell types, comparing communication across conditions, asking which ligand drives a receiver response, or deciding which CCC method and resource to trust.

fridrichmethod Bundle

Use when working with LaminDB, the open-source lineage-native lakehouse for biological datasets and models. Covers setup, artifact registration, query/search, lineage tracking, validation, ontology-backed annotation with Bionty, collections, branches, storage, and workflow integrations.

fridrichmethod Bundle

Build local BLAST databases and run searches using NCBI BLAST+ command-line tools. Use when running >50 queries, building custom databases with -parse_seqids and -taxid, downloading prebuilt NCBI databases via update_blastdb.pl, choosing -task variants (megablast/dc-megablast/blastn/blastn-short), tuning soft/hard masking, scaling threads, or extracting hits with blastdbcmd. Encodes BLAST v5 vs v4 database format, taxonomy filtering, makeblastdb pitfalls.

26zl Bundle

Conduct red team operations using the Covenant C2 framework for authorized adversary simulation, including listener setup, grunt deployment, task execution, and lateral movement tracking.

26zl Bundle

This skill covers hardening GitHub Actions workflows against supply chain attacks, credential theft, and privilege escalation. It addresses pinning actions to SHA digests, minimizing GITHUB_TOKEN permissions, protecting secrets from exfiltration, preventing script injection in workflow expressions, and implementing required reviewers for workflow changes.

26zl Bundle

Test web application email functionality for SMTP header injection vulnerabilities that allow attackers to inject additional email headers, modify recipients, and abuse contact forms for spam relay.

26zl Bundle

Detect malicious email forwarding rules created by adversaries to maintain persistent access to email communications for intelligence collection and BEC attacks.

26zl Bundle

Analyze Microsoft Outlook PST and OST files for email forensic evidence including message content, headers, attachments, deleted items, and metadata using libpff, pst-utils, and forensic email analysis tools for legal investigations and incident response.

fridrichmethod Bundle

Runs the MS-DIAL preprocessing workflow (peak picking, MS2Dec spectral deconvolution, alignment, gap-filling) and imports the alignment-result table into R or Python with honest filtering. Use when preprocessing LC-MS DDA/DIA (SWATH) raw data with MS-DIAL, deciding MS-DIAL vs XCMS, configuring the MsdialConsoleApp console run, or parsing an MS-DIAL export into a clean feature matrix. For programmatic R peak detection and the feature-table-as-artifact framing see metabolomics/xcms-preprocessing; for lipid annotation mode see metabolomics/lipidomics; for MSI-level confidence honesty see metabolomics/metabolite-annotation; for drift correction and QC see metabolomics/normalization-qc.

fridrichmethod Bundle

Calls DNA base modifications (5mC, 5hmC, 6mA, 4mC) directly from Oxford Nanopore and PacBio HiFi long reads encoded as MM/ML SAM tags, piles them into per-site bedMethyl with modkit (or pb-CpG-tools for PacBio), and produces phased allele-specific methylation. Covers why methylation is a basecalling decision that cannot be recovered later, the MM/ML tag-drop failure that silently zeroes methylation through alignment, the MM ? vs . no-call semantics, 5mC/5hmC resolution vs bisulfite, modkit's 10th-percentile auto-threshold, and the haplotagged ASM workflow. Use when calling 5mC/5hmC/6mA from a modBAM, generating bedMethyl, preserving methylation tags through alignment, doing allele-specific or differential methylation, or QC-ing a modification BAM.

26zl Bundle

Automates the Privacy Impact Assessment (PIA) workflow including data flow mapping, privacy risk scoring matrices, GDPR Article 35 DPIA and CCPA/CPRA alignment checks, data inventory cataloging, and remediation tracking. Implements the NIST Privacy Framework PRAM methodology and ICO DPIA guidance for systematic identification and mitigation of privacy risks across processing activities. Use when conducting privacy assessments for new systems, evaluating regulatory compliance posture, or building automated privacy governance programs.

26zl Bundle

Hunt for adversary persistence via Windows Scheduled Tasks by analyzing task creation events, suspicious task actions, and unusual scheduling patterns.

26zl Bundle

Hunt for adversary persistence and execution via Windows scheduled tasks by analyzing task creation events, suspicious task properties, and unusual execution patterns that indicate T1053.005 abuse.

26zl Bundle

Patch management is the systematic process of identifying, testing, deploying, and verifying software updates to remediate vulnerabilities across an organization's IT infrastructure. An effective patc

26zl Bundle

Identifying flaws in application business logic that allow price manipulation, workflow bypass, and privilege escalation beyond what technical vulnerability scanners can detect.

26zl Bundle

Execute a phased DMARC rollout from p=none monitoring through p=quarantine to p=reject enforcement, ensuring all legitimate email sources are authenticated before blocking unauthorized senders.

26zl Bundle

Email sandboxing detonates suspicious attachments and URLs in isolated environments to detect zero-day malware and evasive phishing payloads. Proofpoint Targeted Attack Protection (TAP) is an industry

paulasilvatech Bundle

Elicits, normalizes, validates, and traces requirements through a complete Spec-Driven Development workflow using EARS. Use when converting notes, PRDs, legacy evidence, or design inputs into FRD/NFRD, SPECIFICATION.md, architecture and task artifacts, traceability matrices, quality gates, or an implementation-ready SDD handoff.

paulasilvatech Bundle

Dispatches authorized GitHub issue-comment commands to read-only repository validation. Use when implementing or validating /check-agents, /help, issue comment authorization, command parsing, or IssueOps workflow behavior.

paulasilvatech Bundle

Elicits, normalizes, validates, and traces requirements through a complete Spec-Driven Development workflow using EARS. Use when converting notes, PRDs, legacy evidence, or design inputs into FRD/NFRD, SPECIFICATION.md, architecture and task artifacts, traceability matrices, quality gates, or an implementation-ready SDD handoff.

paulasilvatech Bundle

Two related workflows for a locally-cloned codebase, in one skill. Use this skill when enforced*** — i.e. whether any workflow is a **required status check /; branch-protection rule** that actually blocks merges, versus one that merely; runs — since that distinction is a manual, human-configured setting that.

paulasilvatech Bundle

Generate commit messages that follow the gitmoji convention (https://gitmoji.dev) by choosing the single best emoji or shortcode for a diff, staged change, or plain-language change description. Use when asked to write a gitmoji commit, add an emoji to a commit message, choose a gitmoji, gitmoji this change, or follow a gitmoji-style commit history. Generates the message only and does not run git commands.

paulasilvatech Skill

Upload, download, and embed GitHub user-attachments with the gh attach extension for screenshots, images, PDFs, zip files, and videos. Use this skill when asked to attach a screenshot to a PR, add an image to an issue, embed before/after media, attach a local file, or download a GitHub attachment.

paulasilvatech Skill

Execute git commit with conventional commit message analysis, intelligent staging, and message generation. Use when user asks to commit changes, create a git commit, or mentions "/commit". Supports: (1) Auto-detecting type and scope from changes, (2) Generating conventional commit messages from diff, (3) Interactive commit with optional type/scope/description overrides, (4) Intelligent file staging for logical grouping

paulasilvatech Bundle

Open a browser-based GitHub pull request dashboard for a date range and role filter using the bundled CLI. Use when the user asks to show my PRs, open PR dashboard, check pull request status, see requested reviews, assigned PRs, all involved PRs, or review PR activity for a week, month, year, or explicit date range.

paulasilvatech Skill

Run an interactive task-refinement workflow before implementation by asking targeted questions, exploring the project, defining deliverables, and confirming success criteria. Use when the user asks to act informed, clarify before doing, plan with human input, or refine scope before execution. Requires Joyride human input support.

paulasilvatech Skill

Generate concise, actionable meeting minutes for short internal meetings from notes, transcripts, recordings, or agendas. Use this skill when the user asks for minutes for syncs, standups, design reviews, triage, planning, ad-hoc meetings, decisions, action items, or follow-ups.

26zl Bundle

Implements application whitelisting using Windows AppLocker to restrict unauthorized software execution on endpoints, reducing attack surface from malware, unauthorized tools, and shadow IT. Use when enforcing application control policies, meeting compliance requirements for software restriction, or preventing execution of unsigned or untrusted binaries. Activates for requests involving AppLocker, application whitelisting, software restriction, or executable control.

paulasilvatech Skill

Guide careful implementation through the smallest meaningful change, validation, feedback, and commit-sized increments. Use when the user asks for tiny steps, iterative development, continuous validation, reviewable changes, or a workflow that pauses for feedback before continuing.

paulasilvatech Skill

Review, design, and fix C# async code using Task, Task<T>, ValueTask<T>, cancellation, ConfigureAwait, async streams, and TAP conventions. Use when the user asks for C# async best practices, deadlock fixes, async method naming, parallel awaits, or replacing .Wait(), .Result, and async void.

paulasilvatech Skill

Create, normalize, validate, and check out Git branches following the Conventional Branch specification with feature/, bugfix/, hotfix/, release/, and chore/ prefixes. Use when creating a new branch, naming a branch, or checking branch-name compliance.

paulasilvatech Bundle

Integrate Microsoft Graph SDK in .NET, TypeScript/JavaScript, or Python applications using correct authentication, permissions, SDK clients, pagination, batching, delta queries, change notifications, throttling, and Microsoft 365 resource paths. Use when accessing users, mail, calendar, Teams, OneDrive, SharePoint, groups, search, or other Microsoft 365 data through Graph.