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Testing & QA
Unit tests, integration tests, E2E, QA, validation, and test automation
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Showing 5,497–5,520 of 31,565 skills
- Bio Workflows Merip PipelineOrchestrates an end-to-end MeRIP-seq / m6A-seq analysis from raw FASTQ to differential m6A peak calls and metagene plots, chaining fastp adapter trimming, STAR splice-aware alignment (NO deduplication for non-UMI MeRIP), deepTools replicate-concordance + IP-enrichment QC, PreSeq saturation curves, exomePeak2 (transcript-aware Poisson GLM) peak calling, optional MACS3 broad-peak cross-check, DRACH motif confirmation as a sanity check (NOT a per-peak filter), exomePeak2 differential calling via...Votes: 0GitHub stars: 4
- Bio Workflows Longread Sv PipelineOrchestrates an end-to-end long-read structural-variant pipeline - basecalling to minimap2 alignment (platform-matched preset) to Sniffles2/cuteSV/pbsv calling to optional assembly-based calling (dipcall/PAV) to two-step .snf cohort merging to Truvari benchmarking - chaining ONT and PacBio HiFi runs while handing the SV signal mechanism off to the component skills. Use when running a long-read SV workflow from reads to a benchmarked callset, choosing the minimap2 preset and SV caller by platf...Votes: 0GitHub stars: 4
- Bio Workflows Hic PipelineEnd-to-end Hi-C analysis workflow from FASTQ to compartments, TADs, and loops, with the decision of WHICH features the sequencing depth can support. Covers pairtools read-pair processing and library QC, cooler matrices, ICE balancing and distance-decay expected, A/B compartments, TAD boundaries, loop calling, and the routing of HiChIP/PLAC-seq/Capture Hi-C to protein-directed loop callers. Use when processing Hi-C data end to end, deciding a resolution for a given depth, or choosing between b...Votes: 0GitHub stars: 4
- Bio Workflows Gwas PipelineEnd-to-end GWAS workflow from VCF to association results. Covers PLINK QC, population structure correction, and association testing for case-control or quantitative traits. Use when running genome-wide association studies.Votes: 0GitHub stars: 4
- Bio Workflows Edna PipelineEnd-to-end eDNA metabarcoding from raw amplicons to community ecology. Covers QC, primer removal (mandatory before DADA2 filterAndTrim), denoising with OBITools3 v3 (obi stats plural; DMS-based) or DADA2 ASVs (Callahan 2017), decontam combined method as screening-not-classifier (Davis 2018), tag-jumping with NovaSeq 10x MiSeq caveat (Schnell 2015), Hill-number effective species counts with coverage-based rarefaction (Jost 2006; Chao & Jost 2012; doubling rule), beta-diversity decomposition wi...Votes: 0GitHub stars: 4
- Bio Workflows Cnv PipelineEnd-to-end copy number variant detection workflow from BAM files. Covers CNVkit analysis for exome/targeted sequencing with visualization and annotation. Use when detecting copy number alterations from sequencing data.Votes: 0GitHub stars: 4
- Bio Workflows Clip PipelineEnd-to-end CLIP-seq pipeline from FASTQ to ENCODE-compliant binding sites, single-nucleotide crosslink maps, annotation, motifs, and (optionally) differential binding. Use when running the full Yeo lab eCLIP / iCLIP / iCLIP2 / iCLIP3 / irCLIP / PAR-CLIP analysis with SMInput control, protocol-specific UMI extraction, ENCODE STAR parameters, CLIPper or Skipper peak calling with stringent log2 FC and -log10 p thresholds, IDR rescue and self-consistency QC, and downstream motif registration with...Votes: 0GitHub stars: 4
- Bio Workflows Chipseq PipelineEnd-to-end ChIP-seq workflow from FASTQ files to annotated peaks. Covers QC, alignment, peak calling with MACS3 (or HOMER), and peak annotation with ChIPseeker. Use when processing ChIP-seq data from alignment through peak annotation.Votes: 0GitHub stars: 4
- Smiles ValidationStrict SMILES validation, structural comparison, and modification verification. Catches invalid LLM-generated molecules.Votes: 0GitHub stars: 4
- Tooluniverse Cell Line ProfilingCancer cell-line selection and profiling for experimental model choice. Cross-references DepMap, Cellosaurus, COSMIC, PharmacoDB to deliver identity verification, mutation/CNV profile, gene dependencies, drug sensitivities, and druggable targets. Use to answer 'which cell line should I use for studying gene X?' or 'is this cell line a good model for cancer Y?'. Outputs ranked recommendations with rationale, growth characteristics, and known pitfalls.Votes: 0GitHub stars: 4
- Bio Crispr Screens Screen QcQuality control for pooled CRISPR screens covering library representation, Gini index, log-skew, replicate Pearson and Spearman concordance, essentialome precision-recall AUC against CEGv2 (Hart 2017), Cas9 cut-toxicity diagnostics, copy-number amplicon detection (Aguirre 2016 / Munoz 2016), bottleneck propagation through plasmid pool, infection, selection, and endpoint stages, MOI verification, and DepMap-style screen-quality scoring. Use when assessing screen quality before hit calling, dec...Votes: 0GitHub stars: 4
- Bio Crispr Screens In Vivo ScreensDesigns and analyzes in vivo CRISPR screens in animal tumor models, organoids, and immune-cell adoptive transfers. Covers bottleneck math (250x cells/sgRNA requires ~25M cells implanted; impossible for most syngeneic models, forcing focused libraries), focused library design (Manguso 2017 Nature 547:413 immune screen; Chen 2015 tumor screens), CRISPR-StAR intrinsic-control screening (Uijttewaal 2025 Nat Biotechnol 43:1848), clonal-dynamics-limited detection, tumor-explant DNA recovery, syngen...Votes: 0GitHub stars: 4
- Bio Chipseq QcAssesses ChIP-seq quality across antibody specificity, fragmentation, enrichment, replicate concordance, and library complexity. Computes FRiP, NSC/RSC (phantompeakqualtools), library complexity (NRF/PBC1/PBC2), deepTools plotFingerprint (JS distance, AUC, synthetic JS), ChIPQC, IDR with ENCODE Nself/Nt rules, and detects hyper-ChIPable artifacts. Use when validating an antibody, diagnosing failed peak calls, deciding whether to proceed with downstream analysis, grading against ENCODE thresho...Votes: 0GitHub stars: 4
- Bio Alignment ValidationValidate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other post-alignment metrics. Use when verifying alignment data quality before variant calling or quantification.Votes: 0GitHub stars: 4
- Parallax Portfolio BuilderBuild a portfolio from a natural language investment thesis. Constructs universe, scores, checks redundancy, and outputs allocation-ready list via Parallax MCP tools. Supports `--augment-silent` mode to fill active house view gaps from Parallax data for the current portfolio (saved view never mutates). Trigger for that mode: 'fill house view gaps from Parallax data for this portfolio'. NOT for analyzing existing portfolios (use /parallax-client-review), not for screening without allocation (u...Votes: 0GitHub stars: 5
- Parallax House View DiffInterface spec for verifying that a house view actually changes downstream portfolio output. Trigger: 'did the house view shift my portfolio output?' Describes the dual-leg paired-call protocol and output contract. NOT for loading or making a view (use /parallax-load-house-view or /parallax-make-house-view), not for comparing two saved views (use /parallax-make-house-view --compare). Calibration and reference runner are internal to Parallax.Votes: 0GitHub stars: 5
- Parallax House View AttributionEx-post house-view performance attribution: did the active (or an archived) view add value over its effective window? Reconstructs the tilted-vs-neutral portfolio decision from the reasoning-chain archive, fetches realized returns via Parallax MCP tools, and decomposes the active return into per-tilt-group contributions (Shapley) plus a selection residual. Read-only against the view; emits a report bundle and one `attribution` audit row. NOT for forward-looking drift monitoring (use /parallax...Votes: 0GitHub stars: 5
- Parallax Scenario AnalysisReact to a news event or scenario: assess portfolio exposure, macro regime shift, sector impact, identify most-exposed holdings, find rotation candidates, and output an information-framed action analysis via Parallax MCP tools. Also surfaces under PM/RIA vocabulary: 'stress book', 'scenario suite', 'stress test' (e.g., rates +100bps, USD shock, 2008 / 2020 / 2022 replays). Requires a portfolio and a scenario description. NOT for routine morning briefs (use /parallax-morning-brief), not for ma...Votes: 0GitHub stars: 5
- Parallax Portfolio CheckupIndividual investor portfolio checkup: health flags, factor scores, redundancy, macro context, and plain-language recommendations via Parallax MCP tools. Holdings as [{symbol, weight}]. NOT for fund manager briefs (use /parallax-morning-brief), not for client reviews (use /parallax-client-review), not for drawdown attribution (use /parallax-explain-portfolio), not for trade recommendations (use /parallax-rebalance), not for single stocks (use /parallax-should-i-buy).Votes: 0GitHub stars: 5
- Parallax Morning BriefFund manager morning brief: market regime, macro outlook, portfolio health, and key holding news via Parallax MCP tools. Provide portfolio as [{symbol, weight}] in RIC format. NOT for individual stock analysis (use /parallax-should-i-buy), not for client portfolio review (use /parallax-client-review), not for a desk-wide call list across many books (use /parallax-desk-call-list), not for retail health checks (use /parallax-portfolio-checkup), not for backtesting (use /backtest).Votes: 0GitHub stars: 5
- Wordpress Plugin DevelopmentWordPress plugin development workflow covering plugin architecture, hooks, admin interfaces, REST API, and security best practices.Votes: 0GitHub stars: 36
- Web3 TestingTest smart contracts comprehensively using Hardhat and Foundry with unit tests, integration tests, and mainnet forking. Use when testing Solidity contracts, setting up blockchain test suites, or va...Votes: 0GitHub stars: 36
- Temporal Python TestingTest Temporal workflows with pytest, time-skipping, and mocking strategies. Covers unit testing, integration testing, replay testing, and local development setup. Use when implementing Temporal wor...Votes: 0GitHub stars: 36
- Test FixingRun tests and systematically fix all failing tests using smart error grouping. Use when user asks to fix failing tests, mentions test failures, runs test suite and failures occur, or requests to ma...Votes: 0GitHub stars: 36