12,203 skills found · Page 31 of 407
K-Dense-AI / onekgpdQueries the 1000 Genomes Project dataset (3,202 whole-genome-sequenced individuals, GRCh38) at the level of individual participants
K-Dense-AI / opentrons-integrationAuthors, reviews, migrates, simulates, and troubleshoots official Opentrons Python Protocol API v2 protocols for Flex and OT-2 robots. Use for robot-specific liquid handling, deck and labware setup, pipettes, modules, runtime parameters, liquid classes, and Opentrons App analysis.
K-Dense-AI / paper-lookupSearches 18 scholarly APIs for papers, preprints, citations, open-access full text, repository records, and journal OA status, and returns results with reproducible provenance.
K-Dense-AI / paperclipPaperclip API key from https://paperclip.gxl.ai/keys. Existing OAuth credentials also work; installation and help do not require a key.
K-Dense-AI / pathogen-variant-surveillanceQueries public GenSpectrum LAPIS data for pathogen genomic surveillance, current lineage nomenclature, weekly sequence proportions, reporting delays, and descriptive mutation frequencies.
K-Dense-AI / pathway-enrichmentPerforms pathway and gene-set enrichment analysis on gene lists or ranked gene data and interprets the results. Used when the user has a set of genes (differentially expressed genes from PyDESeq2/Scanpy, CRISPR-screen hits, cluster marker genes, proteomics hits) and wants to know which biological pa…
K-Dense-AI / peer-reviewPrepares evidence-bounded, constructive peer-review drafts and structured manuscript assessments. Supports authorized review of scientific manuscripts, protocols, preprints, or research proposals; reporting-guideline selection; claim–evidence checks; methods, statistics, reproducibility, ethics, fig…
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.
