542 skills · sorted by relevance
SSTI playbook. Use when template expressions, server-side rendering, preview features, or templating engines may evaluate attacker-controlled content.
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Server-Side Template Injection (SSTI) occurs when user input is embedded directly into a template engine (Jinja2, Twig, Freemarker, Pebble, Velocity, Smarty, Mako) and evaluated, enabling remote code execution. Detect via math expressions `{{7*7}}` returning `49`, or `${7*7}`, `<%= 7*7 %>`. Leads to full RCE via template sandbox escape, Python `__class__.__mro__` traversal, and Java reflection chains. Tools: tplmap, Burp Suite.
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Exploit insecure deserialization in Node.js applications (specifically targeting libraries like `node-serialize`) by crafting malicious Immediately Invoked Function Expressions (IIFE) hidden within serialized JSON objects to achieve Remote Code Execution (RCE).
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Use when auditing GitHub Actions workflows for script injection vulnerabilities via unsanitized context expressions. Trigger on: "github actions injection", "workflow injection", "head_ref injection", "github context injection", "pwn request", "github.head_ref", "github.event.pull_request.title", "github.event.issue.body", pull_request_target workflows, run: steps interpolating GitHub context variables, CI/CD script injection, GitHub Actions security audit.
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Use when a task needs the judgment of a Bioinformatics Scientist — designing a differential-expression or GWAS analysis with correct multiple-testing correction, calling and triaging variants from NGS data using genotype-likelihood confidence rather than raw allele counts, interpreting a BLAST/DIAMOND homology search, choosing or building a genomics pipeline (aligner, caller, normalization method) for a specific data-generating process, or judging whether a computational-biology analysis's statistical design actually supports the biological claim being made. Distinct from a bioinformatics-technician (executes and QC-gates an established pipeline someone else designed) and a data-scientist (general product/experimentation judgment, not genomics-specific statistics) — this role owns which method and statistical model a genomics question requires, and why.
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Generates valid Cloud Monitoring ListTimeSeries requests and aggregation specifications from metric descriptors and resource parameters. Use when asked to create, generate, format, or build ListTimeSeries requests, JSON payloads, filter expressions, or aligner/reducer aggregations for Cloud Monitoring metrics and charts. Don't use for metric discovery or metric selection.
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Integrate multiple ENCODE data types (RNA-seq, ATAC-seq, Histone ChIP-seq, TF ChIP-seq) for a tissue/cell type to build a comprehensive regulatory landscape. Use when the user wants to answer "what are the enhancers, promoters, and regulatory elements active in my tissue, and which transcription factors control them?" by layering expression, chromatin accessibility, histone marks, and TF binding data. Follows the Mawla et al. 2023 framework for cross-assay integration of islet cell type-specific data. Handles chromatin state annotation (ChromHMM), enhancer-gene linkage, TF motif enrichment, and cell type-specific regulatory element identification. Use for ANY multi-omic analysis, enhancer discovery, regulatory network construction, or epigenomic characterization using ENCODE data.
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Assess the scientific integrity and trustworthiness of publications before relying on their findings. Use this skill whenever evaluating a paper for a workflow, citing a study, building an analysis on published methods, or when a user asks about the reliability of a study. Checks for formal retractions, corrections, expressions of concern, and — critically — informal contradictions where subsequent studies failed to reproduce key findings. Integrates with PubMed, bioRxiv, and Consensus to provide a trust assessment. Use this skill for ANY publication evaluation, retraction checking, author reliability assessment, or when a user says "can I trust this paper", "is this study reliable", "has this been refuted", or "check this publication".
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Use when designing, reviewing, or troubleshooting Salesforce formula fields. Triggers: 'formula field', 'cross-object formula', 'null handling', 'compile size', 'HYPERLINK', 'IMAGE', 'why is formula slow', 'formulaTreatBlanksAs', 'BlankAsZero', 'blank field handling', 'field-meta.xml formula', 'CustomField formula deploy', 'formula returns blank', 'formula field read-only on data load'. NOT for a formula field slowing a SOQL query or blocking an index — use apex/formula-field-performance-and-limits. NOT for Formula resources inside a Flow — use flow/flow-formula-and-expression-patterns.
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Use this skill when designing or building CRM Analytics Data Prep recipes — including node selection, join patterns, bucket field configuration, formula expressions, and scheduling. Triggers: 'build a recipe', 'join datasets in analytics', 'bucket a measure field', 'schedule a recipe', 'data prep transformation'. NOT for dataflow JSON and its node types — use admin/analytics-dataflow-development. NOT for tuning a slow or oversized dataset — use data/analytics-dataset-optimization.
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Use this skill when building, debugging, or optimizing CRM Analytics dataflows — defining node types (sfdcDigest, Append, Augment, computeExpression, computeRelative, Flatten, dim2mea, sfdcRegister), scheduling runs, handling run failures, and tuning performance. NOT for doing the same transformation in a Data Prep recipe — use admin/analytics-recipe-design. NOT for dataset field types, refresh schedules, or row limits — use admin/analytics-dataset-management.
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Use when monitoring, diagnosing, or managing Batch Apex, Scheduled Apex, Queueable, and Flow scheduled jobs: Setup > Apex Jobs, AsyncApexJob queries, concurrent limits, failure detection, and notification patterns. NOT for writing the Batch or Schedulable class itself — use apex/batch-apex-patterns or apex/apex-scheduled-jobs. NOT for BatchApexErrorEvent alerting in code — use apex/scheduled-apex-failure-detection-and-monitoring. Trigger keywords: Setup > Scheduled Jobs, Apex Flex Queue, CronTrigger, CronJobDetail, FlowInterview, System.abortJob, System.schedule, CRON expression, Holding status, BLOCKED state, reschedule after sandbox refresh, scheduled job runbook.
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Use when enabling, configuring, or monitoring Change Data Capture (CDC) entity selection, channel enrichment, and delivery usage limits from an admin perspective. Covers the PlatformEventChannel and PlatformEventChannelMember metadata, the standard ChangeEvents channel, custom __chn data channels, enrichedFields, filterExpression, destructive deselection, and PlatformEventUsageMetric / EventBusSubscriber monitoring. Trigger keywords: change data capture, CDC, entity selection, change event, platform event channel, channel member, enrichment, event delivery allocation. NOT for writing an Apex change-event trigger — use apex/change-data-capture-apex. NOT for subscribing an external system over Pub/Sub or CometD — use integration/change-data-capture-integration.
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Type design analysis — encapsulation, invariant expression, usefulness, and enforcement.
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Orchestrate AI coding agents (Claude Code, Codex, OpenCode) in isolated sandboxes using the @ai-hero/sandcastle SDK. Use when the user needs to (1) run agents AFK in Docker/Podman containers, (2) build multi-agent pipelines with plan-execute-review patterns, (3) run parallel agents on separate worktrees, (4) create iterative agent loops with maxIterations, (5) extract structured output from agent runs, (6) set up sandcastle in a new or existing project, or (7) write prompt files with template args and shell expressions.
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Multi-age family playing in a park, golden-hour lighting, candid expressions, using reference photos
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Use when building Grafana dashboards backed by Prometheus, Loki, or Tempo, designing PromQL/LogQL queries, wiring template variables, setting alert rules, building SLO dashboards, or maintaining dashboards as code. Triggers: rate() vs increase() confusion, irate vs rate, label_replace, recording rules, alerting rule expressions, multi-dimensional template variables, ad-hoc filters, dashboard JSON model, provisioning via Terraform/grafonnet, p99 / histogram_quantile usage. NOT for Datadog/New Relic dashboards (vendor-specific), Grafana plugin development, or Loki ingestion pipeline tuning.
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Differential abundance (DA) and differential state (DS) analysis for flow and mass cytometry - tests which cell populations change in frequency or marker expression between conditions using diffcyt (edgeR/voom/GLMM for DA, limma/LMM for DS), with cydar, CITRUS, and compositional methods (sccomp, scCODA, DCATS) as alternatives. Covers the sample-is-the-experimental-unit principle, design/contrast and mixed-model formulas, compositionality of cluster proportions, and FDR across clusters. Use when comparing populations between groups, choosing a DA method, handling paired/batch designs, or deciding whether compositional correction is needed.
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Infer transcription factor regulons from single-cell RNA-seq with pySCENIC by combining GRNBoost2 co-expression, cisTarget motif-enrichment pruning, and AUCell per-cell activity scoring. Covers the motif-pruning-as-directionality principle, regulon specificity scoring, run-to-run stability, and database/species matching. Use when identifying TF regulons, scoring TF activity per cell, finding master regulators of cell identity, or comparing regulon activity across conditions. For enhancer-driven multiomic GRNs see multiomics-grn; for bulk inference and VIPER protein-activity see grn-inference.
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Simulate transcription factor perturbation effects on cell state in silico with CellOracle and Dynamo, and predict transcriptional responses to genetic perturbations with GEARS, scGen, and CPA. Covers the direction-not-magnitude principle, local-linear validity, the GRN/velocity error it inherits, baseline discipline (mean and additive baselines), and the validation gap. Use when predicting TF knockout or overexpression effects, ranking driver TFs for fate transitions, or planning perturbation experiments. For GRN construction see multiomics-grn; for experimental Perturb-seq see single-cell/perturb-seq.
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Normalizes and transforms RNA-seq count matrices for DE, visualization, clustering, and ML. Covers between-sample (TMM, TMMwsp, RLE/median-of-ratios, upper quartile), within-sample (TPM, FPKM/RPKM), variance-stabilizing (VST, rlog, log-CPM), GC-content correction (cqn, EDASeq), and single-cell (scran deconvolution, scanpy normalize_total). Encodes the composition-bias rationale, the "most genes not DE" assumption and its catastrophic failure modes (MYC amplification, apoptosis, viral host shutoff, prokaryotic stress), the "lengthScaledTPM is not TPM" naming trap, the "TPM is not for DE" rule, the blind=TRUE vs FALSE decision, ERCC spike-in normalization (SBN), and the single-cell zero-inflation breakdown of TMM/RLE. Use when choosing or applying normalization, debugging shifted-MA-plot diagnostics, handling zero-heavy single-cell data, or correcting GC bias.
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Maps between gene identifier systems (Ensembl, Entrez, HGNC symbol, UniProt, RefSeq, MANE) using AnnotationDbi, biomaRt, mygene, pyensembl, and Ensembl REST. Encodes Ensembl version stripping with GENCODE _PAR_Y preservation, the Ziemann 2016 Excel autocorrect debacle and Bruford 2020 HGNC renames (SEPT*->SEPTIN*, MARCH*->MARCHF*, MARC*->MTARC*, DEC1->DELEC1), OCT4/POU5F1 alias resolution, biomaRt archive endpoints for release pinning, the `filters` (plural) gotcha, MANE Select for clinical reporting, cross-species orthology via Ensembl Compara / OMA / OrthoDB, and tx2gene construction for tximport. Use when converting gene IDs across systems, handling renamed symbols, building tx2gene, pinning to a specific Ensembl release for reproducibility, or mapping cross-species orthologs.
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Calculates statistical power for high-dimensional genomics experiments (bulk RNA-seq, scRNA-seq, ATAC-seq, ChIP-seq, methylation, proteomics) under negative-binomial count models using RNASeqPower, PROPER, and simulation via powsimR, distinguishing per-gene from marginal (transcriptome-wide) power, the role of mean expression and dispersion, and the sequencing-depth-versus-replicate tradeoff. Covers simulation as the honest default for overdispersed counts, FDR-aware average power versus single-test power, observed/post-hoc power as an anti-pattern, and the winner's-curse / Type-S / Type-M consequences of underpowering. Use when planning replicate number for a sequencing experiment, deciding whether to add depth or samples, choosing closed-form versus simulation power, estimating power from pilot dispersions, or justifying replication in a grant. For clinical-trial power see clinical-biostatistics/power-and-sample-size; for the inverse sample-size question see experimental-design/sample-size.
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Designs genomics experiments so technical nuisance variation (batch, lane, plate, flow cell, operator, reagent lot, processing day) is balanced against the biological variable of interest and therefore estimable rather than confounded, using constrained sample-to-batch assignment (designit, OSAT), the confounder/mediator/collider distinction, and the principle that no post-hoc correction recovers a fully confounded design. Covers detecting hidden batches with surrogate variable analysis, a decision table for downstream correction (ComBat-seq, RUVSeq, SVA) whose execution is deferred to differential-expression/batch-correction, and reproducibility metadata. Use when assigning samples to sequencing batches/lanes/plates, avoiding batch-condition confounding, deciding whether a design is salvageable by correction, choosing a correction method, or estimating the number of hidden batches. For the experimental unit, randomization, and blocking concepts see experimental-design/randomization-blocking.
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