Executing Analysis

Design experiments and studies BEFORE data is collected — choosing a design, randomizing, blocking, and laying out treatment combinations so results are interpretable. Use whenever someone is planning a study, asks how to assign subjects/samples to groups, mentions randomization, blocking, stratification, controls, factorial or fractional-factorial designs, design of experiments (DOE), screening many factors, response-surface optimization, crossover or repeated-measures or split-plot designs, cluster/group randomization, Latin squares, plate layouts, batch/run-order effects, replication vs. pseudoreplication, or sequential/adaptive/group-sequential designs. Trigger even for informal phrasings like "how should I set up this experiment", "how do I avoid confounding", "what's the best way to test these 6 factors", or "assign these mice to conditions". For computing the sample size or power once the design is chosen, use statistical-power; for analyzing data already collected, use statistical-analysis.

Local document and PDF parsing that returns spatial text with bounding boxes. Use for extracting text from PDFs, DOCX, Office files, and images; running OCR on scans; producing layout-preserved JSON for RAG; batch-ingesting folders of papers; or rendering pages to PNG for multimodal agents. Distinguishing capabilities are per-token bounding boxes, page raster output, and fully local processing with no cloud API.

Operator toolkit for nf-core/pacsomatic matched tumor-normal workflows from BAM inputs. Use this skill when the user needs to validate run inputs, generate pacsomatic-compliant samplesheets, prepare reproducible Nextflow launch artifacts, run locally or submit to schedulers (LSF/Slurm/PBS/SGE), and triage execution failures. Triggers on requests to run pacsomatic, prepare launch commands/scripts, perform dry-run checks, or troubleshoot pipeline startup and scheduler submission errors.

ktx's knowledge base - wiki pages for durable, reusable business knowledge. Covers capture workflow for user preferences, metric definitions, organizational conventions, and cross-references between wiki pages and semantic-layer sources. Loaded by the post-turn memory-agent only. The research agent reads wiki via `wiki_read`/`wiki_search` but does not write it.

Workflow and tools for adding new entries from temp.md to the section files. Includes legend format, section reference, code tools, and common pitfalls. USE FOR: Adding new resources to the knowledge base. DO NOT USE FOR: Editing existing entries or restructuring sections.

Workflow for updating the popular LLM applications pool (section/x_llm_apps.md) using get_app_list_by_github_star.py. Covers full refresh, alternate exports, topic tuning, and common pitfalls. USE FOR: Refreshing the ranked GitHub applications list linked from applications.md. DO NOT USE FOR: Hand-curating application entries inside applications.md or adding GitHub star badges to the generated file.