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Claude Skills by lilinji
github.com/lilinji193 skills0 installs365 views
- 21 Cfr Part 11Provide implementation guidance for electronic records/signatures (ER/ES) compliance: access control, audit trails, data integrity, and validation expectations in medical device software and supporting tools.Votes: 0GitHub stars: 8
- Audit LoggingDefine what and how to log for medical devices: security/safety events, integrity, protection, and retention of logs for compliance and forensics.Votes: 0GitHub stars: 8
- AuthenticationDefine secure user/device authentication, session management, and RBAC suitable for medical device risk profiles.Votes: 0GitHub stars: 8
- Automated TestingDefine how to automate tests (unit, integration, system/HIL where feasible) in CI/CD pipelines for medical devices with gating and evidence capture.Votes: 0GitHub stars: 8
- Bio BasecallingConvert raw Nanopore signal data (FAST5/POD5) to nucleotide sequences using Dorado basecaller. Covers model selection, GPU acceleration, modified base detection, and quality filtering. Use when processing raw Nanopore data before alignment. Note: Guppy is deprecated; use Dorado for all new analyses.Votes: 0GitHub stars: 8
- Bio OrchestratorMeta-agent that routes bioinformatics requests to specialised sub-skills. Handles file type detection, analysis planning, report generation, and reproducibility export.Votes: 0GitHub stars: 8
- Ble MedicalGuide secure, reliable BLE implementation for medical devices handling PHI/therapy control: services, pairing/bonding, LE Secure Connections, privacy, and performance.Votes: 0GitHub stars: 8
- Change ControlDefine controlled process for software changes: requests, impact analysis, approvals, verification, and configuration management in regulated contexts.Votes: 0GitHub stars: 8
- Claw Ancestry PcaAncestry decomposition PCA against the Simons Genome Diversity ProjectVotes: 0GitHub stars: 8
- Claw MetagenomicsShotgun metagenomics profiling — taxonomy, resistome, and functional pathwaysVotes: 0GitHub stars: 8
- Claw Semantic SimSemantic Similarity Index for disease research literature using PubMedBERT embeddingsVotes: 0GitHub stars: 8
- ClinpgxQuery the ClinPGx API for pharmacogenomic gene-drug data, clinical annotations, CPIC guidelines, and FDA drug labelsVotes: 0GitHub stars: 8
- Code CommentsProvide conventions for code comments that support traceability to requirements, risks, and tests, while maintaining clarity and brevity.Votes: 0GitHub stars: 8
- Code CoverageMeasure and enforce coverage appropriate to safety class: statement/branch and MC/DC where applicable, with documented exclusions.Votes: 0GitHub stars: 8
- Data IntegrityEnsure integrity of data in storage and transmission using checksums/CRCs/ECC, validation, and redundancy where needed for medical devices.Votes: 0GitHub stars: 8
- Defensive DesignApply defensive coding techniques to prevent, detect, and safely handle abnormal conditions in safety-relevant software.Votes: 0GitHub stars: 8
- Design DocsGuide creation and maintenance of Software Architecture (SAD) and Design Descriptions (SDD) that support safety, traceability, and compliance.Votes: 0GitHub stars: 8
- Drug PhotoMedication photo to personalised PGx dosage card via Claude vision — snap a pill, get genotype-informed guidanceVotes: 0GitHub stars: 8
- Dynamic AnalysisDetect runtime defects (memory, concurrency, timing, performance, power) via dynamic tools and instrumentation in medical device software.Votes: 0GitHub stars: 8
- Embedded CDefine C coding practices aligned with MISRA C and medical device safety needs: type safety, control flow, memory management, interrupts, and static analysis.Votes: 0GitHub stars: 8
- Embedded CppDefine a constrained C++ subset suitable for medical device firmware, aligned to MISRA C++ guidance: safe types, RAII, limited dynamic features, and predictable behavior.Votes: 0GitHub stars: 8
- EncryptionGuide selection and use of cryptography for medical devices: algorithms, key derivation, data at rest/in transit, library choice, and FIPS considerations.Votes: 0GitHub stars: 8
- Equity ScorerCompute HEIM diversity and equity metrics from VCF or ancestry data. Generates heterozygosity, FST, PCA plots, and a composite HEIM Equity Score with markdown reports.Votes: 0GitHub stars: 8
- Eu MdrProvide actionable guidance for software under EU MDR, focusing on classification (Rule 11), technical documentation expectations, UDI for software, PMS/PMCF needs, and alignment with MDCG guidance.Votes: 0GitHub stars: 8
- Fault ToleranceProvide patterns for detecting, containing, and recovering from faults in medical device software, scaled to safety class.Votes: 0GitHub stars: 8
- Fda PremarketGuide preparation of FDA premarket submission software documentation (510(k), De Novo, PMA), including documentation depth determination, required documents, cybersecurity, SBOM, interoperability, and post-market commitments.Votes: 0GitHub stars: 8
- Fuzz TestingUncover robustness and security issues by fuzzing inputs/protocols relevant to medical devices (parsers, IPC, network/BLE/USB).Votes: 0GitHub stars: 8
- Galaxy BridgeGalaxy tool discovery, intelligent recommendation, and execution — 8,000+ bioinformatics tools from usegalaxy.org with multi-signal scoring and workflow suggestionsVotes: 0GitHub stars: 8
- Genome CompareCompare your genome to George Church (PGP-1) and estimate ancestry composition via IBS and EM admixtureVotes: 0GitHub stars: 8
- Gwas LookupFederated variant lookup across 9 genomic databases — GWAS Catalog, Open Targets, PheWeb (UKB, FinnGen, BBJ), GTEx, eQTL Catalogue, and more.Votes: 0GitHub stars: 8
- Gwas PrsCalculate polygenic risk scores from DTC genetic data using the PGS CatalogVotes: 0GitHub stars: 8
- Hardware AbstractionProvide patterns for HAL design that enable testability, portability, and safety: clear interfaces, separation from application logic, and mockability.Votes: 0GitHub stars: 8
- Hardware In LoopValidate software with real or representative hardware, sensors, actuators, and timing, to uncover integration and safety issues not visible in simulation.Votes: 0GitHub stars: 8
- Iec 62304Provide actionable guidance to implement IEC 62304 lifecycle controls across planning, development, verification, release, and maintenance, with class-dependent rigor for Class A/B/C software items.Votes: 0GitHub stars: 8
- Iec 62443Apply IEC 62443 concepts (secure development lifecycle, component requirements, security levels) to networked medical devices, ensuring threat-aware design, implementation, and verification of cybersecurity controls.Votes: 0GitHub stars: 8
- Inline DocsProvide concise, high-value inline documentation practices (comments and short docblocks) that improve safety, maintainability, and traceability without cluttering code.Votes: 0GitHub stars: 8
- Integration TestingValidate interactions between software components and hardware interfaces, ensuring interfaces, protocols, and data flows behave correctly in realistic configurations.Votes: 0GitHub stars: 8
- InteroperabilityEnable safe and standards-aligned interoperability: HL7 FHIR/IHE profiles, data formats, terminology mapping, and API design for medical data exchange.Votes: 0GitHub stars: 8
- Interrupt HandlingDefine safe interrupt design: short ISRs, deferred work, priority assignment, critical section management, and testing strategies.Votes: 0GitHub stars: 8
- Iso 14971Integrate ISO 14971:2019 risk management into software development: hazard identification, risk evaluation, control implementation in code, verification of effectiveness, and documentation of residual risk.Votes: 0GitHub stars: 8
- Key ManagementDefine generation, storage, rotation, revocation, and provisioning of cryptographic keys for medical devices, supporting secure boot, OTA, and comms.Votes: 0GitHub stars: 8
- LabstepInteract with the Labstep electronic lab notebook API using labstepPy. Query experiments, protocols, resources, inventory, and other lab entities.Votes: 0GitHub stars: 8
- Lit SynthesizerSearch PubMed and bioRxiv, summarise papers with LLM, build citation graphs, and generate literature review sections.Votes: 0GitHub stars: 8
- Bio Crispr Screens Prime Editing ScreensDesigns and analyzes pooled prime-editor (PE) screens for installing precise genetic variants without bystander confounding. Covers pegRNA design with PRIDICT and PRIDICT2 for predicting per-pegRNA editing efficiency, pegRNA architecture (spacer + scaffold + PBS + RTT), PE2/PE3/PE3b/PEmax variants, MOSAIC in situ saturation mutagenesis, the PRIME pooled-screen methodology (Ren 2023; ~3,699 ClinVar variant screens), chromatin context as a major locus-level determinant of PE efficiency, scaffol...Votes: 0GitHub stars: 8
- Bio Epidemiological Genomics Pathogen TypingAssigns isolate identity at the right resolution for the question -- ANI/Mash species triage, 7-locus MLST historical comparability, cgMLST/wgMLST outbreak resolution (chewBBACA, BIGSdb, Ridom SeqSphere, EnteroBase HierCC), in-silico serotyping (SISTR/SeqSero2 Salmonella, SerotypeFinder E. coli, Kaptive Klebsiella, SeroBA pneumococcus, spa+SCCmec S. aureus), and lineage callers (TB-Profiler/Mykrobe barcode for MTBC, Pangolin + Nextclade for SARS-CoV-2, PopPUNK GPSC for S. pneumoniae). Use whe...Votes: 0GitHub stars: 8
- Bio Epidemiological Genomics PhylodynamicsEstimates time-scaled phylogenies, molecular-clock rates, effective reproduction number R_e, and population dynamics from dated pathogen genomes using TreeTime (maximum-likelihood) and BEAST2 (Bayesian; strict/relaxed clocks; coalescent, Bayesian-Skyline, Skygrid, Birth-Death-Skyline, and sampled-ancestor priors; structured coalescent via MASCOT). Covers root-to-tip clock QC via TempEst, date-randomisation tests, recombination masking via Gubbins/ClonalFrameML before clock inference for recom...Votes: 0GitHub stars: 8
- Bio Flow Cytometry Differential AnalysisDifferential 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 wh...Votes: 0GitHub stars: 8
- Bio Gatk Variant CallingCall germline SNPs and indels with GATK HaplotypeCaller and the GVCF joint-genotyping workflow. Covers the local-reassembly + PairHMM mechanism (why HC beats pileup callers on indels), the -ERC GVCF reference-confidence model and <NON_REF> allele, BQSR-vs-DRAGSTR and --dragen-mode error modeling, allele-specific (AS_) annotations, and edge cases (ploidy, Mutect2 mitochondria mode, sex chromosomes/PAR, contamination gating). Use when deciding whether to use HaplotypeCaller vs a pileup or DRAGE...Votes: 0GitHub stars: 8
- Bio Long Read Sequencing Haplotype PhasingPhases small variants, SVs, and methylation from Oxford Nanopore and PacBio long reads (read-backed/physical phasing) with WhatsHap, LongPhase, or HiPhase, and haplotags the BAM (HP/PS tags) for allele-resolved downstream analysis. Covers why phase blocks break at het-sparse gaps (read length x heterozygosity), why phasing the VCF is useless until the BAM is haplotagged, the GT-pipe/PS and read HP/PS tag spec, reporting block N50 with switch error, the diploid-assumption/CNV/haploid-region tr...Votes: 0GitHub stars: 8
- Bio Long Read SplicingAnalyzes alternative splicing from PacBio Iso-Seq (HiFi, Kinnex/MAS-Iso-seq) and Oxford Nanopore (direct cDNA, direct RNA, R10.4.1+) long-read RNA-seq with full-isoform resolution. Tools include FLAIR (correct/collapse/quantify/diffSplice for PacBio + ONT), IsoQuant (de-novo or annotation-guided isoform discovery 2024 SOTA), Bambu (annotation-aware Bayesian discovery + quantification with Novel Discovery Rate), SQANTI3 (isoform classification: FSM/ISM/NIC/NNC + artifact flags), rMATS-long (ev...Votes: 0GitHub stars: 8