14,567 skills found · Page 34 of 486
K-Dense-AI / phylogeneticsBuilds and analyzes phylogenetic trees using MAFFT multiple sequence alignment, IQ-TREE maximum likelihood with ModelFinder and branch support, and FastTree approximate inference. Uses ETE3 for tree summaries and visualization.
K-Dense-AI / pkpd-modelingPharmacokinetic and pharmacodynamic modelling and simulation - non-compartmental analysis, compartmental and population PK, PK/PD and exposure-response, TMDD, PBPK orientation, bioequivalence, allometric scaling and first-in-human dose, drug interaction prediction, and Bayesian therapeutic drug moni…
K-Dense-AI / polars-bioPerforms genomic interval overlap, nearest, merge, coverage, complement and subtraction on Polars DataFrames, and reads or writes BED, VCF, BCF, BAM, CRAM, GFF, GTF, FASTA and FASTQ data.
K-Dense-AI / primer-designDesigns and audits PCR and RT-qPCR primers with Primer3, explicit thermodynamic conditions, reference-based off-target amplification searches, and traceable sequence coordinates.
K-Dense-AI / pufferlibVersion-aware guidance for PufferLib reinforcement-learning environments, vectorization, policies, PuffeRL training, evaluation, and safe checkpoint review. Covers the native 5.0 build and environment API, published 3.0.0 Gymnasium/PettingZoo adaptation, and a pinned historical 4.0 profile.
K-Dense-AI / pydeseq2Performs bulk RNA-seq differential expression analysis with PyDESeq2, including count validation, formula designs, explicit contrasts, Wald tests, FDR correction, coefficient-matched LFC shrinkage, and result visualization. Use for PyDESeq2 or Python DESeq2 workflows with biological replicates.
K-Dense-AI / pydicomReads, inspects, writes, transforms, and preflights local DICOM datasets and pixel data. Applies to DICOM metadata, transfer syntaxes, compression plugins, frames, private elements, JSON, and bounded de-identification review.
K-Dense-AI / pymatgenAnalyzes, validates, converts, and transforms materials structures and computed materials data with pymatgen. Use for local phase diagrams, symmetry sensitivity, electronic-structure I/O, and bounded Materials Project queries.
K-Dense-AI / pysamProvides Python/HTSlib workflows for genomic files. Used when reading, querying, filtering, or writing SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ, or tabix data with pysam, including pileup, coverage, indexing, and CRAM references.
K-Dense-AI / pytdcProvides Therapeutics Data Commons workflows through PyTDC for registry discovery, dataset access, task-aware splits, evaluator metrics, benchmark groups, and bounded molecular-oracle scoring
K-Dense-AI / qutipSimulate and audit closed and open quantum-system models with QuTiP 5, including deterministic, trajectory, steady-state, spectral, and phase-space workflows. Use for local quantum-dynamics work where physical assumptions, dimensions, and numerical convergence must be explicit.
K-Dense-AI / relsa-severity-assessmentSupports multivariate severity assessment and exploratory endpoint-time score forecasting for laboratory animal studies using the RELSA (RELative Severity Assessment) score and ARIMA-based foRcast forecasting
K-Dense-AI / scanpyPerforms Scanpy single-cell RNA-seq QC, normalization, HVG selection, PCA/UMAP/t-SNE, clustering, exploratory marker ranking, pseudobulk preparation, visualization, and Seurat or SingleCellExperiment RDS conversion to h5ad.
K-Dense-AI / scientific-brainstormingFacilitates evidence-aware scientific ideation with independent generation, structured discussion, explicit assumptions, transparent evaluation, adversarial review, and decision logs.
K-Dense-AI / scientific-visualizationCreates and audits truthful, accessible, publication-ready scientific figures with Matplotlib, Seaborn, or Plotly. Use it for figure design, multi-panel layouts, uncertainty and missing-data displays, color/contrast review, image metadata validation, and journal export planning.
K-Dense-AI / scientific-writingDrafts, revises, and audits scientific manuscripts or reports with explicit evidence provenance, reporting-guideline coverage, authorship accountability, confidentiality controls, and local consistency checks.
K-Dense-AI / scikit-bioBiological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.
K-Dense-AI / scikit-survivalBuilds, evaluates, and audits right-censored or competing-risk survival workflows with scikit-survival, including leakage-safe preprocessing, model selection, probability prediction, and censoring-aware metrics.
K-Dense-AI / shapExplain and audit machine-learning predictions with SHAP. Use for selecting SHAP explainers and maskers, computing and validating feature attributions, handling multi-output explanations, and producing local or global SHAP visualizations.
K-Dense-AI / simpyBuilds, inspects, tests, and analyzes bounded process-based discrete-event simulations with SimPy. Use for event scheduling, resource queues, interrupts, monitoring, independent replications, warm-up, and reproducible output analysis.
K-Dense-AI / statistical-analysisGuided statistical analysis for research data - test selection, assumption checking, effect sizes, power analysis, Bayesian alternatives, and APA-formatted reporting
K-Dense-AI / statistical-powerCalculates sample sizes and statistical power for study planning. Applies when someone asks "how many subjects/samples/replicates do I need", wants an a priori power analysis, a minimum detectable effect (MDE), a power curve, or needs to justify a sample size for a grant, IRB protocol, or pre-regist…
K-Dense-AI / tiledbvcfStores and retrieves genomic variant calls with TileDB-VCF. Use for indexed single-sample VCF/BCF ingestion, incremental cohorts, region and sample queries, streaming results, allele statistics, QC, and VCF/BCF export locally or through TileDB Cloud.
K-Dense-AI / timesfm-forecastingPerforms zero-shot time-series forecasting with Google's TimesFM, including regular-grid CSV preparation, quantile forecasts, XReg covariates, and held-out evaluation.
K-Dense-AI / 13c-metabolic-fluxEstimates intracellular metabolic fluxes from steady-state carbon-13 isotope-tracing measurements using validated atom maps, mfapy isotope simulation, constrained multistart fitting, and flux-profile diagnostics.
K-Dense-AI / adaptyvUses the Adaptyv Bio Foundry API and Python SDK to design protein characterization experiments, estimate costs, submit sequences, monitor laboratory progress, and retrieve results.
K-Dense-AI / arboretoInfers candidate gene regulatory networks from bulk or single-cell expression data using AertsLab Arboreto GRNBoost2 and GENIE3. Use for transcription factor-target association ranking, compatible Dask execution, sparse expression inputs, and network stability checks.
K-Dense-AI / bidsOrganizes, queries, validates, and converts Brain Imaging Data Structure (BIDS) datasets. Supports organizing neuroscience and biomedical data (MRI, EEG, MEG, iEEG, PET, microscopy, NIRS, motion capture, EMG, MR spectroscopy, behavioral), querying BIDS layouts, validating compliance, converting DICO…
K-Dense-AI / clinical-decision-supportPrepares and validates research-only clinical decision-support evaluation, evidence-profile, cohort, survival, biomarker/model, privacy, and governance artifacts. Supports aggregate or synthetic research documentation and traceability, excluding patient care and live clinical operation.
K-Dense-AI / database-lookupQueries documented public database APIs with explicit endpoints, filters, pagination, and provenance. Used when a scientific, regulatory, financial, or other database-backed fact must be retrieved reproducibly from a named source rather than inferred from general knowledge.
