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Plan or run DNA analysis to find small genetic changes in tumors, using tumor samples alone or paired with normal tissue. Check sample pairing, contamination, data quality, filtering, and annotations that add information to detected variants.
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Prepare detailed 3D materials that remain clear in close-up views. The skill guides texture resolution, physically based material maps, surface mapping, filtering, and progressive loading while checking download size and GPU memory use.
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Integrate Octav API to retrieve crypto balances, transaction history, and portfolio snapshots across multiple blockchains. Track holdings in DeFi, blockchain-based financial services, and filter transactions by network, date, or activity for use in applications.
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Write and troubleshoot native Python in n8n Code nodes. Covers data filtering and transformation, migration from older Python code, valid return formats, and restricted execution environments, including cases where errors pass unprocessed input downstream.
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Search LinkedIn jobs by keywords, location, work arrangement, employment type, experience level, posting date, and company. Collect job descriptions, applicant counts, direct links, and salary information when provided to organize potential opportunities.
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Filter Excel rows using conditions across several numeric columns. Count rows across sheets, convert selected fields to numbers, remove duplicate rows and records with missing identifiers, then export the filtered results to a new workbook.
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Query GitHub issues and extract or summarize selected fields using jq, a JSON filtering tool. Inspect data structure and size before retrieving detailed results, then filter by status, author, labels, comments, or creation date.
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Query GitHub pull requests by author, status, or review needs, and extract selected fields as JSON. Inspect the data structure and size first, then use jq, a JSON filtering tool, to refine results.
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Query GitHub Discussions and extract titles, authors, categories, or answer status. First inspect the data structure and size, then use jq, a JSON filtering tool, to select relevant discussions, sort updates, or count entries by category.
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Generate structured CSV security audit reports from vulnerability data with proper filtering and formatting. This skill covers CSV schema design for security reports, using Python csv.DictWriter, severity-based filtering, and field mapping from JSON to tabular format.
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Data conditioning techniques for gravitational wave detector data. Use when preprocessing raw detector strain data before matched filtering, including high-pass filtering, resampling, removing filter wraparound artifacts, and estimating power spectral density (PSD). Works with PyCBC TimeSeries data.
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Extracts, filters, annotates, and exports differential expression results from DESeq2 or edgeR with proper handling of padj=NA (independent filtering, Cook's outliers, all-zero), multiple-testing correction choice (BH vs Storey q-value vs IHW vs lfsr), TREAT vs post-hoc fold-change filtering, p-value histogram diagnostics, gene annotation via org.db/biomaRt/mygene, GSEA preranked input, ORA background construction, replication reality (Schurch 2016 small-n result), and SABV/sex-stratified reporting. Use when extracting and interpreting DE results, troubleshooting padj=NA, choosing FDR method, preparing ranked lists for pathway analysis, annotating gene IDs, or comparing DESeq2 vs edgeR outputs.
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Build Sankey, alluvial, river, and CONSORT-style flow diagrams to visualize cohort transitions, cell-state changes, or pipeline filtering using ggalluvial, networkD3, plotly, and consort. Use when showing how entities move between categories across timepoints (cell states, drug response classes, patient flow through a trial) or filtering pipelines (variants filtered through QC stages).
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Analyzes single-cell pooled CRISPR screens (Perturb-seq, CROP-seq, Perturb-CITE-seq, ECCITE-seq, multiome) where each cell carries an sgRNA and a scRNA-seq / surface-protein / chromatin readout. Covers experimental design (direct-capture Perturb-seq Dixit 2016 vs CROP-seq 3'UTR-barcoded Datlinger 2017 vs ECCITE-seq vs Multiome), MOI for sgRNA assignment, escaper-cell filtering (Mixscape, Papalexi 2021), SCEPTRE NB GLM + permutation for low-MOI (Barry 2024 Genome Biol 25:124), the Pertpy framework, factor decomposition, genome-scale Perturb-seq (Replogle 2022 Cell, 2.5M cells), and per-perturbation single-cell DE. Use when running a single-cell CRISPR screen, choosing direct-capture vs CROP-seq architecture, filtering escaper cells, performing single-cell DE, integrating Perturb-seq with pathway analysis, scaling to GW CRISPRi via Replogle protocol, or analyzing multi-omics screens.
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Annotate copy number variant segments with overlapping genes, dosage-sensitivity scores, cancer driver databases, population frequencies, and clinical-variant content. Covers bedtools/pybedtools interval intersection, AnnotSV comprehensive annotation and ranking, ClinGen haploinsufficiency/triplosensitivity scoring, gnomAD-SV/DGV frequency filtering, COSMIC Cancer Gene Census, and ClinVar overlap. Use when interpreting which genes a CNV affects, distinguishing the driver gene of a focal event from passengers, filtering against population CNVs, separating whole-gene from partial-gene overlap, or preparing CNVs for clinical classification.
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Perform time-frequency analysis in MATLAB using CWT, STFT, synchrosqueezing, reassignment, wavelet coherence, cross spectrogram, EMD/VMD, multiresolution analysis, and time-frequency filtering. Triggers on: time-frequency, spectrogram, scalogram, cwt, stft, istft, fsst, wsst, wcoherence, xspectrogram, modwt, modwtmra, modwpt, emd, vmd, hht, tffilt, dgt, gabor, instantaneous frequency, synchrosqueezing, reassignment, ridge extraction, wavelet coherence, cross spectrum, mode decomposition, signal decomposition, time-frequency filtering.
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Design and implement adaptive filters using DSP System Toolbox System objects. Use when working with adaptive filtering, system identification, noise cancellation, echo cancellation, active noise control (ANC), channel equalization, inverse system identification, or adaptive prediction. Covers dsp.LMSFilter, dsp.RLSFilter, dsp.FilteredXLMSFilter, dsp.FrequencyDomainAdaptiveFilter, dsp.AffineProjectionFilter, dsp.BlockLMSFilter, dsp.AdaptiveLatticeFilter, dsp.FastTransversalFilter, maxstep(), and algorithm selection for adaptive filtering problems. Replaces deprecated adaptfilt.* objects (removed R2020a).
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Run MATLAB test suites and analyze results, including test filtering, parallel execution, result diagnostics, code coverage collection, gap analysis, and CI/CD with buildtool. Use when running tests, filtering test suites, analyzing test failures, checking, collecting, or analyzing coverage, justifying uncovered code, or configuring CI pipelines. Do NOT use for writing, generating, or structuring tests. Do NOT use for Simulink coverage or Simulink testing workflows.
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Connect MATLAB to Databricks via Spark (Databricks Connect) or JDBC (Database Toolbox). Use when setting up the MATLAB Interface for Databricks, configuring authentication (OauthU2M, OauthM2M, PAT), creating Spark sessions with getDatabricksSession(), reading Unity Catalog tables with server-side filtering, creating JDBC connections with databricks.JDBCConnection or StandaloneJDBCConnection, connecting to SQL Warehouses, selecting JDBC drivers (Simba/OSS), or writing data back to Databricks. Triggers on: Databricks Connect, Spark from MATLAB, getDatabricksSession, .databrickscfg, databricks.JDBCConnection, StandaloneJDBCConnection, SQLWarehouse, Databricks JDBC, Databricks cluster, large table server-side filtering.
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Performs quality control on single-cell RNA-seq data (.h5ad or .h5 files) using scverse best practices with MAD-based filtering and comprehensive visualizations. Use when users request QC analysis, filtering low-quality cells, assessing data quality, or following scverse/scanpy best practices for single-cell analysis.
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Enforce "No Exploit, No Report" policy with PoC construction standards, false-positive filtering, and evidence collection per vulnerability class across backend, frontend, and mobile. Use when validating security findings, constructing exploit proofs, filtering false positives, or writing pentest findings.
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DepMap CRISPR gene effect (Chronos) analysis: sign convention for essentiality, per-gene NaN-safe Spearman correlation, data loading/alignment. For general NaN-safe correlation see nan-safe-correlation; for quality filtering see degenerate-input-filtering.
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Builds flexible API filtering and sorting systems with query parameter parsing, validation, and security. Use when implementing search endpoints, building data grids, or creating dynamic query APIs.
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Build Sankey, alluvial, river, and CONSORT-style flow diagrams to visualize cohort transitions, cell-state changes, or pipeline filtering using ggalluvial, networkD3, plotly, and consort. Use when showing how entities move between categories across timepoints (cell states, drug response classes, patient flow through a trial) or filtering pipelines (variants filtered through QC stages).
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