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Claude Skills by jaechang-hits
github.com/jaechang-hits208 skills2 installs445 views
- Snakemake Workflow EnginePython-based workflow manager for reproducible, scalable pipelines. Define rules with file-based dependencies; Snakemake resolves execution order and parallelism. Runs local, SLURM, LSF, AWS, GCP via profiles; per-rule conda/Singularity envs. For NGS pipelines, ML training, and multi-step file processing. Use Nextflow for Groovy dataflow or nf-core integration.Votes: 0GitHub stars: 368
- Spikeinterface ElectrophysiologyUnified Python framework for extracellular electrophysiology. Load 20+ formats (SpikeGLX, OpenEphys, NWB, Intan, Maxwell, Blackrock), preprocess, run 10+ sorters (Kilosort4, SpykingCircus2, Tridesclous, MountainSort5) via one API, compute quality metrics (SNR, ISI, firing rate), compare sorters, export NWB/Phy. For format-agnostic multi-sorter workflows. For Neuropixels-specific PSTH/decoding use neuropixels.Votes: 0GitHub stars: 368
- Sympy Symbolic MathSymbolic math in Python: exact algebra, calculus (derivatives, integrals, limits), equation solving, symbolic matrices, ODEs, code gen (lambdify, C/Fortran). Use for exact symbolic results. For numerical use numpy/scipy; for stats use statsmodels.Votes: 0GitHub stars: 368
- Torch Geometric Graph Neural NetworksPyTorch Geometric (PyG) for graph neural networks: node/graph classification, link prediction with GCN, GAT, GraphSAGE, GIN. Message passing, mini-batches, heterogeneous graphs, neighbor sampling, explainability. Supports molecules (QM9, MoleculeNet), social/knowledge graphs, 3D point clouds. For non-graph DL use PyTorch; for classical graph algorithms use NetworkX.Votes: 0GitHub stars: 368
- Transformers Bio NlpHuggingFace Transformers with biomedical LMs (BioBERT, PubMedBERT, BioGPT, BioMedLM) for scientific NLP: NER (genes, diseases, chemicals), relation extraction, QA, text classification, abstract summarization. Covers loading, biomedical tokenization, inference pipelines, fine-tuning. Alternatives: spaCy en_core_sci_lg (rule-based NER), Stanza (biomedical models), NLTK.Votes: 0GitHub stars: 368
- Umap LearnUMAP dimensionality reduction for visualization, clustering prep, and feature engineering. Fast nonlinear manifold learning preserving local and global structure. Standard UMAP (fit/transform, sklearn-compatible), supervised/semi-supervised, Parametric UMAP (NN encoder/decoder, TensorFlow), DensMAP (density), AlignedUMAP (temporal/batch). 15+ distance metrics, custom Numba metrics, precomputed distances. For linear reduction use PCA; for neighborhood graphs use sklearn NearestNeighbors.Votes: 0GitHub stars: 368
- Uspto DatabaseAccess USPTO patent data via PatentsView REST API and Google Patents Public Data (BigQuery). Search by inventor, assignee, CPC, or keywords; download metadata and claims; analyze portfolios; track tech trends. For IP landscape analysis, competitor monitoring, prior art search, and tech forecasting in life sciences and biotech.Votes: 0GitHub stars: 368
- Vaex DataframesOut-of-core DataFrame for billion-row data via lazy evaluation and memory-mapped files. Use when data exceeds RAM (10 GB–TB) for fast aggregation, filtering, virtual columns, and visualization without loading. Supports HDF5, Arrow, Parquet, CSV with cloud (S3, GCS, Azure). Built-in ML transformers (scaling, PCA, K-means). In-memory: polars; distributed: dask.Votes: 0GitHub stars: 368
- Zarr PythonChunked N-D arrays with compression and cloud storage. NumPy-style indexing. Backends: local, S3, GCS, ZIP, memory. Dask/Xarray integration for parallel and labeled computation. For lineage use lamindb; for labeled arrays use xarray.Votes: 0GitHub stars: 368
- Biorxiv DatabaseQuery bioRxiv/medRxiv preprints via REST API. Search by DOI, category, or date range; retrieve metadata (title, abstract, authors, category, DOI, version history) and PDFs. No auth. For peer-reviewed biomedical use pubmed-database; broader scholarly search use openalex-database.Votes: 0GitHub stars: 368
- Cancer Research Figure GuideCancer Research (AACR) figures: resolution (300-1200 DPI), formats (EPS/TIFF/AI), hierarchical panel labels (Ai, Aii, Bi), figure/table limits, legend requirements with replicate counts.Votes: 0GitHub stars: 368
- Cell Figure GuideCell (Cell Press) figure preparation: resolution (300-1000 DPI), formats (TIFF/PDF), RGB color, Avenir/Arial fonts, uppercase panel labels, strict image manipulation policies.Votes: 0GitHub stars: 368
- Citation ManagementSelecting a reference manager and applying citation styles. Compares Zotero, Mendeley, EndNote, Paperpile; covers APA/Vancouver/ACS/Nature styles, DOI management, citation tracking, and Word/Google Docs/LaTeX integration. Use when setting up a reference workflow or fixing citation formatting.Votes: 0GitHub stars: 368
- Clinical Decision Support DocumentsGuidelines for clinical decision support (CDS) documents: biomarker-stratified cohort analyses and GRADE-graded treatment reports. Covers structure, executive summaries, evidence grading (1A–2C), stats (HR, CI, survival), and biomarker integration. Use for pharma research docs, clinical guidelines, regulatory submissions.Votes: 0GitHub stars: 368
- Elife Figure GuideeLife figure preparation: file formats (TIFF/EPS/PDF), striking image requirements (1800x900 px), figure supplement naming, and image screening policy treating selective enhancement as misconduct.Votes: 0GitHub stars: 368
- General Figure GuideUniversal QA checklist for generated scientific plots: overlapping labels, clipped text, missing axes/legends, overcrowded data, and cross-journal resolution/format guidance.Votes: 0GitHub stars: 368
- Hypothesis GenerationStructured hypothesis formulation: turn observations into testable hypotheses with predictions, propose mechanisms, design experiments. Follows the scientific method. Use scientific-brainstorming for open ideation; hypogenic for automated LLM hypothesis testing on datasets.Votes: 0GitHub stars: 368
- Lancet Figure GuideThe Lancet figure preparation: resolution (300+ DPI at 120%), preferred editable formats (PowerPoint/Word/SVG), column widths (75/154 mm), Times New Roman, in-house redraw policy.Votes: 0GitHub stars: 368
- Latex Research PostersResearch posters in LaTeX using beamerposter, tikzposter, or baposter. Layout, typography, color schemes, figure integration, accessibility, and QA for conferences. Includes templates. For figure generation use matplotlib-scientific-plotting or plotly-interactive-plots.Votes: 0GitHub stars: 368
- Literature ReviewConducting systematic, scoping, and narrative literature reviews. Covers PRISMA/PRISMA-ScR protocols, search strategy (Boolean, MeSH), database selection (PubMed, Scopus, Web of Science, Embase), screening, data extraction, evidence synthesis (narrative, meta-analysis, thematic), and reporting. Use when planning or executing a formal literature review.Votes: 0GitHub stars: 368
- Nature Figure GuideNature figure preparation: resolution (300+ DPI), formats (AI/EPS/TIFF), RGB color, Helvetica/Arial fonts, lowercase panel labels, image integrity requirements.Votes: 0GitHub stars: 368
- Nejm Figure GuideNEJM figure preparation: resolution (300-1200 DPI), editable vector formats (AI/EPS/SVG), in-house medical illustration policy, and strict image integrity requirements.Votes: 0GitHub stars: 368
- Openalex DatabaseQuery OpenAlex REST API for 250M+ scholarly works, authors, institutions, journals, concepts. Search by keyword, author, DOI, ORCID, or ID; filter by year, OA, citations, field; retrieve citations, references, author disambiguation. Free, no auth. For PubMed use pubmed-database; preprints use biorxiv-database.Votes: 0GitHub stars: 368
- Peer Review MethodologyStructured peer review of manuscripts and grants. 7-stage evaluation: initial assessment, section review, statistical rigor, reproducibility, figure integrity, ethics, writing. Covers CONSORT/STROBE/PRISMA and report structure. For evidence quality see scientific-critical-thinking; scoring see scholar-evaluation.Votes: 0GitHub stars: 368
- Pnas Figure GuidePNAS figure preparation: resolution (300-1000 PPI), formats (TIFF/EPS/PDF), strict RGB-only color, Arial/Helvetica fonts, italicized uppercase panel labels, automated image screening.Votes: 0GitHub stars: 368
- Science Figure GuideScience (AAAS) figure preparation: resolution (150-300+ DPI), formats (PDF/EPS/TIFF), RGB color, Myriad/Helvetica fonts, strict image manipulation policies including gamma adjustment disclosure.Votes: 0GitHub stars: 368
- Scientific BrainstormingStructured ideation methods: SCAMPER, Six Thinking Hats, Morphological Analysis, TRIZ, Biomimicry, plus more. Decision framework for picking methods by challenge type (stuck, improving, systematic exploration, contradiction). Use when generating research ideas or exploring interdisciplinary connections.Votes: 0GitHub stars: 368
- Scientific Critical ThinkingEvaluating scientific evidence and claims. Covers study design hierarchy (RCT to expert opinion), effect sizes (OR, RR, NNT, Cohen's d), confounding, p-value vs clinical significance, GRADE quality assessment, reproducibility, and bias types (selection, information, confounding, reporting). Use when reading a paper or assessing claims.Votes: 0GitHub stars: 368
- Scientific Literature SearchSystematic strategies for searching scientific literature across PubMed, arXiv, Google Scholar, and AI-assisted tools. Covers PICO framework for clinical questions, three-tiered search (database-specific, AI-assisted, content extraction), PubMed field tags and MeSH, boolean query construction, and full-text extraction. Use when planning a literature search or choosing a search tier.Votes: 0GitHub stars: 368
- Scientific Manuscript WritingScientific manuscript writing: IMRAD, citation styles (APA/AMA/Vancouver/IEEE), figures/tables, reporting guidelines (CONSORT/STROBE/PRISMA/ARRIVE), writing principles (clarity/conciseness/accuracy), venue-specific style. For LaTeX see companion assets.Votes: 0GitHub stars: 368
- Scientific SchematicsDesigning scientific schematics, diagrams, and graphical abstracts. Covers tool selection (BioRender, Inkscape, Affinity, PowerPoint), design principles for pathway diagrams, mechanism schematics, experimental workflows, and journal graphical abstracts. Includes composition, icon sourcing, color for biological entities, and accessibility. Use when creating illustrative (not data-driven) scientific figures.Votes: 0GitHub stars: 368
- Scientific SlidesScientific presentations for conferences, seminars, thesis defenses, and grant pitches. Slide design, talk structure, timing, data viz for slides, QA. PowerPoint and LaTeX Beamer. For posters use latex-research-posters.Votes: 0GitHub stars: 368
- Alphafold Database AccessAccess AlphaFold DB's 200M+ predicted structures by UniProt ID. Download PDB/mmCIF, analyze pLDDT/PAE, bulk-fetch proteomes via Google Cloud. For experimental structures use PDB; for prediction use ColabFold or ESMFold.Votes: 0GitHub stars: 368
- Autodock Vina DockingMolecular docking with AutoDock Vina (Python API). Receptor/ligand prep (Meeko + RDKit), grid box, docking, pose and binding energy analysis, and batch virtual screening.Votes: 0GitHub stars: 368
- Chembl Database BioactivityQuery ChEMBL (2M+ compounds, 19M+ bioactivity measurements, 13K+ targets) via the public REST/JSON API with plain `requests` — no SDK install required. Search compounds, retrieve IC50/Ki/EC50 bioactivities, find target inhibitors, run SAR, access drug mechanism/indication data.Votes: 0GitHub stars: 368
- Clinicaltrials Database SearchQuery ClinicalTrials.gov API v2 for trial data. Search by condition, drug/intervention, location, sponsor, or phase; fetch details by NCT ID; filter by status; paginate; export CSV. For clinical research, patient matching, and trial portfolio analysis.Votes: 0GitHub stars: 368
- Dailymed DatabaseQuery FDA drug labels (DailyMed) via REST API. Search structured product labels (SPLs) by name, NDC, set ID, or RxCUI; get indications, dosage, warnings, adverse reactions, packaging. No auth. For adverse events use fda-database; for DDIs use ddinter-database.Votes: 0GitHub stars: 368
- Datamol CheminformaticsPythonic RDKit wrapper with sensible defaults for drug discovery. SMILES parsing, standardization, descriptors, fingerprints, similarity, clustering, diversity selection, scaffold analysis, BRICS/RECAP fragmentation, 3D conformers, and visualization. Returns native rdkit.Chem.Mol. Prefer datamol for standard workflows; use RDKit directly for advanced control.Votes: 0GitHub stars: 368
- Ddinter DatabaseQuery DDInter drug-drug interactions via REST API (1.7M+ interactions, 2,400+ drugs). Search by drug name/ID for severity (major/moderate/minor), mechanisms, and clinical recommendations. No auth. For FDA labeling use dailymed-database; for pharmacogenomics use clinpgx-database.Votes: 0GitHub stars: 368
- DeepchemDeep learning for drug discovery. 60+ models (GCN, GAT, AttentiveFP, MPNN, ChemBERTa, GROVER), 50+ featurizers, MoleculeNet benchmarks, HPO, transfer learning. Unified load-featurize-split-train-evaluate API. For fingerprints use rdkit-cheminformatics; for featurization-only use molfeat.Votes: 0GitHub stars: 368
- DiffdockDiffusion-based docking that predicts protein-ligand poses without a predefined site. Use for blind docking, when traditional docking fails, or exploring multiple binding modes. Pipeline: prep protein (PDB) and ligand (SMILES/SDF), run inference, analyze confidence-ranked poses.Votes: 0GitHub stars: 368
- Sciagent Skill CreatorScaffold a new SciAgent-Skills entry. Picks pipeline/toolkit/database/guide template, creates skills/{category}/{name}/SKILL.md with valid frontmatter, appends the registry.yaml entry, runs validation. Enforces name uniqueness, kebab-case, description keyword rules, schema rules from AGENTS.md. TRIGGER when user says (any language): "add a SciAgent skill", "add a skill for <X>", "create new skill", "create a SKILL.md for <X>", "scaffold a skill", "new skill entry", "register a skill", "신규 sk...Votes: 0GitHub stars: 368
- Molecular Visualization 3dmol3Dmol.js WebGL molecular visualization emitted as self-contained HTML. Render structures (PDB/SDF/XYZ/MOL2/cube) with stick, sphere, cartoon, line, and surface styles; animate trajectories with a frame-delay (interval, ms) control; and animate vibrational normal modes via vibrate() from per-atom dx/dy/dz displacements or from precomputed frames. Output standalone HTML that loads 3Dmol from a CDN, with optional play/pause and speed controls. Use for transition-state imaginary-mode animations, ...Votes: 0GitHub stars: 368
- MultipanelAssemble multiple plots into ONE publication-ready multi-panel journal figure (e.g. Figure 1 with panels A, B, C). Use whenever the user asks to combine, compose, or lay out several plots as a single composite figure — newly plotted from data or from already-rendered panels the user supplies (PNG/PDF). Ask the user to pick one of two approaches: (1) redraw every panel into one unified figure using independent, tightly packed `subfigures` (each sized to its own labels, so axes need NOT align),...Votes: 0GitHub stars: 368
- Omics Plottingomics-plotting: publication-style figure authoring for omics / bioinformatics results with matplotlib / seaborn. Read this before writing any plotting or figure code in any omics analysis — RNA-seq, proteomics, single-cell, variant, or database results — not only when a plot is explicitly requested: whenever an analysis will produce a figure, load this first and follow its recipes. Covers volcano, MA, expression / correlation heatmap, GSEA bar / dot plot, box / violin / bar / ridgeline, PCA /...Votes: 0GitHub stars: 368
- Bwa Mem2 Dna AlignerFast short-read DNA aligner for WGS/WES/ChIP-seq. 2× faster BWA-MEM successor; outputs SAM/BAM with read group headers for GATK. Primary plus supplementary records for chimeric reads. Use STAR for RNA-seq splice-aware alignment; Bowtie2 is a comparable alternative.Votes: 0GitHub stars: 368
- Pysam Genomic FilesRead/write SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ. Region queries, pileup, variant filtering, read groups. Python htslib wrapper exposing samtools/bcftools CLI. Use STAR/BWA for alignment; GATK/DeepVariant for variant calling.Votes: 0GitHub stars: 368
- Samtools Bam ProcessingCLI toolkit for SAM/BAM/CRAM: sort, index, convert, filter, QC alignments. Core commands: view, sort, index, flagstat, stats, depth, markdup, merge. Required between alignment and variant/peak calling. Use pysam for Python-native BAM access; deeptools for normalized coverage tracks.Votes: 0GitHub stars: 368
- Star Rna Seq AlignerSplice-aware RNA-seq aligner producing sorted BAM and splice junction tables. Builds genome index, runs two-pass alignment for better junctions. Outputs sorted BAM, junctions (SJ.out.tab), stats (Log.final.out), optional gene counts. Use Salmon for fast pseudoalignment; STAR when a BAM is needed for variant calling, IGV, or ENCODE pipelines.Votes: 0GitHub stars: 368
- Bakta Genome AnnotationAnnotate bacterial and archaeal genomes and plasmids with Bakta's Prodigal/HMM/diamond pipeline. Identifies CDS, ncRNA, tRNA, rRNA, tmRNA, sORFs, CRISPR arrays, oriC/oriV/oriT, and gaps against a curated UniRef-derived database. Produces NCBI-compatible GFF3, GenBank, EMBL, JSON, FASTA, TSV, and a circular genome plot. Use Prokka for legacy pipelines or non-bacterial kingdoms; PGAP for NCBI GenBank submission.Votes: 0GitHub stars: 368