jaechang-hits/sciagent-skills

jaechang-hits/sciagent-skills · .claude/skills/sciagent-skill-creator/SKILL.md · Scaffold a new SciAgent-Skills entry. Picks pipeline/toolkit/database/guide template, creates…

jaechang-hits/sciagent-skills · AGENTS.md

jaechang-hits/sciagent-skills · CLAUDE.md

jaechang-hits/sciagent-skills · integration-templates/AGENTS.md

jaechang-hits/sciagent-skills · legacy/opentrons-integration/SKILL.md · Opentrons Protocol API v2 for OT-2/Flex: Python protocols for pipetting, serial dilutions, PCR, plate replication…

jaechang-hits/sciagent-skills · legacy/plotly-interactive-visualization/SKILL.md · Interactive visualization with Plotly. 40+ chart types (scatter, line, heatmap, 3D, geographic) with hover, zoom, pan…

jaechang-hits/sciagent-skills · legacy/seaborn-statistical-visualization/SKILL.md · Statistical visualization on matplotlib + pandas. Distributions (histplot, kdeplot, violin, box), relational (scatter…

jaechang-hits/sciagent-skills · legacy/single-cell-annotation/SKILL.md · Best practices for single-cell RNA-seq cell type annotation including marker-based, reference-based, and automated…

jaechang-hits/sciagent-skills · skills/biostatistics/pymc-bayesian-modeling/SKILL.md · Bayesian modeling with PyMC 5: priors, likelihood, NUTS/ADVI sampling, diagnostics (R-hat, ESS), LOO/WAIC comparison…

jaechang-hits/sciagent-skills · skills/biostatistics/scikit-survival-analysis/SKILL.md · Time-to-event modeling with scikit-survival: Cox PH (elastic net), Random Survival Forests, Boosting, SVMs for censored…

jaechang-hits/sciagent-skills · skills/biostatistics/statistical-analysis/SKILL.md · Guided statistical analysis: test choice, assumption checks, effect sizes, power, APA reporting. Pick tests, verify…

jaechang-hits/sciagent-skills · skills/biostatistics/statsmodels-statistical-modeling/SKILL.md · Python statistical modeling: regression (OLS, WLS, GLM), discrete (Logit, Poisson, NegBin), time series (ARIMA…

jaechang-hits/sciagent-skills · skills/cell-biology/cellpose-cell-segmentation/SKILL.md · DL cell/nucleus segmentation for fluorescence and brightfield microscopy. Pre-trained models (cyto3, nuclei, tissuenet)…

jaechang-hits/sciagent-skills · skills/cell-biology/flowio-flow-cytometry/SKILL.md · Parse/write FCS (Flow Cytometry) files v2.0-3.1. Events as NumPy, channel metadata, multi-dataset files, CSV/FCS…

jaechang-hits/sciagent-skills · skills/cell-biology/napari-image-viewer/SKILL.md · Interactive viewer for microscopy. Displays 2D/3D/4D arrays as Image, Labels, Points, Shapes, Tracks layers; supports…

jaechang-hits/sciagent-skills · skills/cell-biology/opencv-bioimage-analysis/SKILL.md · Computer vision for bio-image preprocessing, feature detection, real-time microscopy. Color conversion, morphology…

jaechang-hits/sciagent-skills · skills/cell-biology/pyimagej-fiji-bridge/SKILL.md · Python bridge to ImageJ2/Fiji for macros, plugins (Bio-Formats, TrackMate, Analyze Particles), NumPy↔ImagePlus/ImgLib2…

jaechang-hits/sciagent-skills · skills/cell-biology/scikit-image-processing/SKILL.md · Python image processing for microscopy and bioimage analysis. Read/write images, filter (Gaussian, median, LoG)…

jaechang-hits/sciagent-skills · skills/cell-biology/trackpy-particle-tracking/SKILL.md · Python library for single-particle tracking (SPT) in video microscopy via the Crocker-Grier algorithm. Locate particles…

jaechang-hits/sciagent-skills · skills/data-visualization/matplotlib-scientific-plotting/SKILL.md · Low-level Python plotting for scientific figures: publication-quality line, scatter, bar, heatmap, contour, 3D…

jaechang-hits/sciagent-skills · skills/data-visualization/molecular-visualization-3dmol/SKILL.md · 3Dmol.js WebGL molecular visualization emitted as self-contained HTML. Render structures (PDB/SDF/XYZ/MOL2/cube) with…

jaechang-hits/sciagent-skills · skills/data-visualization/multipanel/SKILL.md · Assemble multiple plots into ONE publication-ready multi-panel journal figure (e.g. Figure 1 with panels A, B, C). Use…

jaechang-hits/sciagent-skills · skills/data-visualization/omics-plotting/SKILL.md · omics-plotting: publication-style figure authoring for omics / bioinformatics results with matplotlib / seaborn. Read…

jaechang-hits/sciagent-skills · skills/data-visualization/plotly-interactive-plots/SKILL.md · Interactive scientific visualization with Plotly. Two APIs: plotly.express (px) for one-liner DataFrame plots…

jaechang-hits/sciagent-skills · skills/data-visualization/scientific-visualization/SKILL.md · Guide for choosing and creating scientific visualizations for publications and talks. Covers chart-type selection by…

jaechang-hits/sciagent-skills · skills/data-visualization/seaborn-statistical-plots/SKILL.md · Statistical visualization on matplotlib with native pandas support. Auto aggregation, CIs, grouping for distributions…

jaechang-hits/sciagent-skills · skills/data-visualization/statistical-significance-annotation/SKILL.md · Guide for annotating statistical significance (p-value asterisks) on comparison plots. Covers standard notation (ns, *…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/alignment/bwa-mem2-dna-aligner/SKILL.md · Fast short-read DNA aligner for WGS/WES/ChIP-seq. 2× faster BWA-MEM successor; outputs SAM/BAM with read group headers…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/alignment/pysam-genomic-files/SKILL.md · Read/write SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ. Region queries, pileup, variant filtering, read groups. Python htslib…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/alignment/samtools-bam-processing/SKILL.md · CLI toolkit for SAM/BAM/CRAM: sort, index, convert, filter, QC alignments. Core commands: view, sort, index, flagstat…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/alignment/star-rna-seq-aligner/SKILL.md · Splice-aware RNA-seq aligner producing sorted BAM and splice junction tables. Builds genome index, runs two-pass…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/annotation/bakta-genome-annotation/SKILL.md · Annotate bacterial and archaeal genomes and plasmids with Bakta's Prodigal/HMM/diamond pipeline. Identifies CDS, ncRNA…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/annotation/prokka-genome-annotation/SKILL.md · Annotate prokaryotic genomes (bacteria, archaea, viruses) via Prokka's BLAST/HMM pipeline. Identifies CDS, rRNA, tRNA…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/annotation/roary-pangenome/SKILL.md · Compute the bacterial pan-genome from Prokka/Bakta GFF3 annotations with Roary's CD-HIT + BLAST + MCL clustering…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/arboreto-grn-inference/SKILL.md · GRN inference from expression via GRNBoost2 (gradient boosting) or GENIE3 (Random Forest). Load matrix, filter by TFs…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/biopython-molecular-biology/SKILL.md · Molecular biology toolkit: sequence manipulation, FASTA/GenBank/PDB I/O, NCBI Entrez, BLAST automation, pairwise/MSA…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/biopython-sequence-analysis/SKILL.md · Biopython sequence analysis: parse FASTA/FASTQ/GenBank/GFF (SeqIO), NCBI Entrez (esearch/efetch/elink), remote/local…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/databases/archs4-database/SKILL.md · Query ARCHS4 REST API for uniformly processed RNA-seq expression, tissue patterns, co-expression across 1M+ human/mouse…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/databases/bioservices-multi-database/SKILL.md · Unified Python interface to 40+ bioinformatics web services: UniProt proteins, KEGG pathways, ChEMBL/ChEBI/PubChem…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/databases/cbioportal-database/SKILL.md · Cancer genomics (TCGA et al.) via cBioPortal REST API. Retrieve somatic mutations, CNAs, expression, clinical data…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/databases/clinpgx-database/SKILL.md · Query the ClinPGx (formerly PharmGKB) REST API plus the CPIC PostgREST companion API for pharmacogenomic clinical…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/databases/clinvar-database/SKILL.md · Query NCBI ClinVar via E-utilities for variant clinical significance, pathogenicity, disease associations. Search by…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/databases/cosmic-database/SKILL.md · Query COSMIC for cancer somatic mutations, gene census, mutational signatures, drug resistance variants. REST API v3.1…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/databases/dbsnp-database/SKILL.md · Query NCBI dbSNP for SNP records by rsID, gene, or region via E-utilities and Variation Services REST API. Retrieve…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/databases/depmap-crispr-essentiality/SKILL.md · DepMap CRISPR gene effect (Chronos) analysis: sign convention for essentiality, per-gene NaN-safe Spearman correlation…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/databases/ena-database/SKILL.md · ENA REST API for sequences, reads, assemblies, and annotations. Portal API search, Browser API retrieval…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/databases/encode-database/SKILL.md · ENCODE Portal REST API for regulatory genomics: TF ChIP-seq, ATAC-seq/DNase-seq peaks, histone marks, and RNA-seq…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/databases/ensembl-database/SKILL.md · Ensembl REST API for gene/transcript/variant annotations in 300+ species. Gene info by symbol/ID, sequence, cross-refs…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/databases/gene-database/SKILL.md · NCBI Gene via E-utilities: curated records across 1M+ taxa. Official symbols, aliases, RefSeq IDs, summaries…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/databases/geo-database/SKILL.md · NCBI GEO access via GEOparse and E-utilities. Search by keyword/organism/platform, download GSE series matrices, parse…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/databases/gget-genomic-databases/SKILL.md · Unified CLI/Python interface to 20+ genomic databases. Gene lookups (Ensembl search/info/seq), BLAST/BLAT, AlphaFold…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/databases/gnomad-database/SKILL.md · gnomAD v4 population variant frequencies via GraphQL API. Allele counts and frequencies stratified by ancestry (AFR…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/databases/gwas-database/SKILL.md · NHGRI-EBI GWAS Catalog REST API for SNP-trait associations from published GWAS. Query studies, associations, variants…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/databases/jaspar-database/SKILL.md · JASPAR 2024 TF binding profiles via REST API and pyJASPAR. Retrieve PFMs/PWMs by TF name, JASPAR ID, species, or…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/databases/kegg-database/SKILL.md · KEGG REST API (academic only). Pathways, genes, compounds, enzymes, diseases, drugs via 7 ops…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/databases/monarch-database/SKILL.md · Monarch Initiative knowledge graph REST API for disease-gene-phenotype associations and cross-species orthology. MONDO…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/databases/mouse-phenome-database/SKILL.md · Retrieve mouse phenotype data from the Jackson Laboratory Mouse Phenome Database (MPD) via its REST API. Browse 520+…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/databases/quickgo-database/SKILL.md · Query EBI QuickGO REST API for GO terms and protein annotations. Fetch term metadata by ID, search by keyword, walk…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/databases/regulomedb-database/SKILL.md · Query RegulomeDB v2 GET REST API to score variants for regulatory function and retrieve overlapping evidence (TF…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/databases/remap-database/SKILL.md · Query ReMap 2022 TF ChIP-seq peak database via REST API and BED downloads. Retrieve TF peaks overlapping a region…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/databases/ucsc-genome-browser/SKILL.md · Query UCSC Genome Browser REST API for DNA sequences, tracks, gene models, and conservation across 100+ assemblies…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/etetoolkit/SKILL.md · ETE Toolkit (ETE3): Python phylogenetic tree analysis and visualization. Parse Newick/NHX/PhyloXML, traverse/annotate…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/homer-motif-analysis/SKILL.md · De novo and known TF motif enrichment in ChIP-seq/ATAC-seq peaks via HOMER. findMotifsGenome.pl finds over-represented…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/interval-ops/bedtools-genomic-intervals/SKILL.md · Genomic interval ops on BED/BAM/GFF/VCF. Find overlaps, merge intervals, compute coverage, extract FASTA, find nearest…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/interval-ops/deeptools-ngs-analysis/SKILL.md · NGS CLI for ChIP/RNA/ATAC-seq. BAM→bigWig with RPGC/CPM/RPKM, sample correlation/PCA, heatmaps/profiles around…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/interval-ops/geniml/SKILL.md · Python library for genomic interval ML. Train/apply region2vec embeddings turning BED regions into vectors, index…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/interval-ops/gtars/SKILL.md · Rust-backed Python library for fast genomic token arithmetic and BED processing. High-performance BED I/O, interval set…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/macs3-peak-calling/SKILL.md · Poisson-model peak caller for ChIP-seq/ATAC-seq BAMs. MACS3 callpeak finds enriched regions (TF sites or histone marks)…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/qc/busco-status-interpretation/SKILL.md · Guide to interpreting BUSCO completeness statuses: why Duplicated BUSCOs count as complete, parsing output files…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/qc/fastp-fastq-preprocessing/SKILL.md · All-in-one FASTQ QC and adapter trimming. Auto-detects Illumina adapters, filters low-quality reads, corrects…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/qc/multiqc-qc-reports/SKILL.md · Aggregates QC from 150+ bioinformatics tools into one interactive HTML report. Scans FastQC, samtools, STAR, HISAT2…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/rnaseq/deseq2-differential-expression/SKILL.md · Bulk RNA-seq DE with R/Bioconductor DESeq2. Negative binomial GLM, empirical Bayes shrinkage, Wald/LRT tests…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/rnaseq/featurecounts-rna-counting/SKILL.md · Counts RNA-seq reads overlapping GTF gene features. Takes sorted STAR BAMs plus GTF; outputs a per-gene tab-delimited…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/rnaseq/gseapy-gene-enrichment/SKILL.md · GSEA and over-representation analysis (ORA) for RNA-seq and proteomics. Wraps Enrichr for ORA against MSigDB, KEGG, GO…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/rnaseq/pydeseq2-differential-expression/SKILL.md · Bulk RNA-seq DE with PyDESeq2: load counts, normalize, fit negative binomial models, Wald test (BH-FDR), LFC shrinkage…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/rnaseq/salmon-rna-quantification/SKILL.md · Ultra-fast RNA-seq transcript/gene quantification via quasi-mapping (no BAM). Builds a k-mer index from transcriptome…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/scikit-bio/SKILL.md · Python library for biology: sequence manipulation (DNA/RNA/protein), pairwise/multiple alignment, phylogenetic trees…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/single-cell/anndata-data-structure/SKILL.md · Annotated matrices for single-cell genomics. Stores X with obs/var metadata, layers, embeddings (obsm/varm), graphs…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/single-cell/celltypist-cell-annotation/SKILL.md · Automated scRNA-seq cell type annotation via pre-trained logistic regression. 45+ models: immune, gut, lung, brain…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/single-cell/cellxgene-census/SKILL.md · Query CELLxGENE Census (61M+ cells). Search by cell type/tissue/disease/organism; get AnnData, stream out-of-core…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/single-cell/harmony-batch-correction/SKILL.md · Harmony batch correction for scRNA-seq and other omics. Removes batch effects from PCA embeddings while preserving…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/single-cell/popv-cell-annotation/SKILL.md · Consensus cell type annotation: runs 10+ algorithms (KNN-Harmony/BBKNN/Scanorama/scVI, CellTypist, ONCLASS, Random…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/single-cell/scanpy-scrna-seq/SKILL.md · scRNA-seq with Scanpy: QC, normalization, HVG selection, PCA, neighborhood graph, UMAP/t-SNE, Leiden clustering…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/single-cell/scvi-tools-single-cell/SKILL.md · Deep generative models for single-cell omics: probabilistic batch correction (scVI), semi-supervised annotation…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/single-cell/single-cell-annotation-guide/SKILL.md · Cell type annotation strategy for scRNA-seq: name clusters manually from canonical markers, transfer labels from a…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/variant/bcftools-variant-manipulation/SKILL.md · CLI for VCF/BCF: filter, merge, annotate, query, normalize, compute stats. Core post-variant-calling: quality…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/variant/cnvkit-copy-number/SKILL.md · Detect somatic CNVs from WES/WGS/targeted BAMs (CNVkit v0.9.x). Bin coverage in target/antitarget regions, normalize vs…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/variant/gatk-variant-calling/SKILL.md · GATK Best Practices for germline SNP/indel calling from WGS/WES BAMs. Per-sample HaplotypeCaller GVCFs…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/variant/plink2-gwas-analysis/SKILL.md · GWAS and population genetics tool. Processes PLINK (.bed/.bim/.fam), VCF, and BGEN; runs QC (MAF, HWE, missingness)…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/variant/snpeff-variant-annotation/SKILL.md · Annotate and filter VCF variants with SnpEff and SnpSift. SnpEff predicts functional effects…

jaechang-hits/sciagent-skills · skills/genomics-bioinformatics/variant/vcf-variant-filtering/SKILL.md · Guide to quality filtering raw VCF files before computing summary stats (Ts/Tv ratio, variant counts, AF…

jaechang-hits/sciagent-skills · skills/lab-automation/benchling-integration/SKILL.md · Benchling R&D Python SDK: CRUD on registry entities (DNA, RNA, proteins, custom), inventory, ELN, workflow automation…

jaechang-hits/sciagent-skills · skills/lab-automation/opentrons-protocol-api/SKILL.md · Python API v2 for Opentrons OT-2/Flex liquid handlers: protocols as Python files with metadata and run(); control…

jaechang-hits/sciagent-skills · skills/lab-automation/protocolsio-integration/SKILL.md · protocols.io REST API: search and fetch wet-lab, bioinformatics, and clinical protocols by keyword, DOI, or category…

jaechang-hits/sciagent-skills · skills/lab-automation/pylabrobot/SKILL.md · Hardware-agnostic Python liquid-handler library: portable scripts run on Hamilton STAR, Tecan Freedom EVO, Opentrons…

jaechang-hits/sciagent-skills · skills/lab-automation/western-blot-quantification/SKILL.md · Protocols and best practices for western blot quantification and analysis including band detection, normalization, and…

jaechang-hits/sciagent-skills · skills/medical-imaging/histolab-wsi-processing/SKILL.md · WSI processing for digital pathology. Tissue detection, tile extraction (random, grid, score-based), filter pipelines…

jaechang-hits/sciagent-skills · skills/medical-imaging/imaging-data-commons/SKILL.md · Query and download NCI Imaging Data Commons (IDC) cancer radiology and pathology datasets via the idc-index Python…

jaechang-hits/sciagent-skills · skills/medical-imaging/nnunet-segmentation/SKILL.md · Medical image segmentation with nnU-Net's self-configuring framework — auto-selects architecture, preprocessing…

jaechang-hits/sciagent-skills · skills/medical-imaging/omero-integration/SKILL.md · Open-source bio-image data management. Use the omero-py client to connect to an OMERO server, retrieve images as numpy…

jaechang-hits/sciagent-skills · skills/medical-imaging/pathml/SKILL.md · Computational pathology toolkit for whole-slide images (WSIs): load slides, extract tiles, stain normalization, nuclear…

jaechang-hits/sciagent-skills · skills/medical-imaging/pydicom-medical-imaging/SKILL.md · Pure Python DICOM for medical imaging (CT, MRI, X-ray, ultrasound). Read/write DICOM, pixels as NumPy, edit tags…

jaechang-hits/sciagent-skills · skills/medical-imaging/simpleitk-image-registration/SKILL.md · Register, segment, filter, resample 3D medical images (MRI, CT, microscopy) via SimpleITK Python; DICOM, NIfTI…

jaechang-hits/sciagent-skills · skills/molecular-biology/plannotate-plasmid-annotation/SKILL.md · Auto-annotate plasmids with features (promoters, terminators, resistance, origins, tags, fluorescent proteins) via…

jaechang-hits/sciagent-skills · skills/molecular-biology/sgrna-design-guide/SKILL.md · Three-tiered sgRNA design guide using validated Addgene sequences, CRISPick pre-computed datasets, or de novo design…

jaechang-hits/sciagent-skills · skills/molecular-biology/viennarna-structure-prediction/SKILL.md · Predict RNA secondary structure, MFE folding, base-pair probabilities, RNA-RNA interactions via ViennaRNA Python…

jaechang-hits/sciagent-skills · skills/proteomics-protein-engineering/adaptyv-bio/SKILL.md · API + Python SDK for ordering cell-free protein expression and binding assays. Submit sequences for expression (10–100…

jaechang-hits/sciagent-skills · skills/proteomics-protein-engineering/esm-protein-language-model/SKILL.md · Protein language models (ESM3, ESM C) for sequence generation, structure prediction, inverse folding, and embeddings…

jaechang-hits/sciagent-skills · skills/proteomics-protein-engineering/hmdb-database/SKILL.md · Parse HMDB (Human Metabolome Database) local XML for metabolite info, chemical properties, biological context, disease…

jaechang-hits/sciagent-skills · skills/proteomics-protein-engineering/interpro-database/SKILL.md · Query InterPro REST API for protein domain architecture, family classification, and member-DB integration. Search…

jaechang-hits/sciagent-skills · skills/proteomics-protein-engineering/matchms-spectral-matching/SKILL.md · MS spectral matching and metabolite ID with matchms. Import spectra (mzML, MGF, MSP, JSON), filter/normalize peaks…

jaechang-hits/sciagent-skills · skills/proteomics-protein-engineering/maxquant-proteomics/SKILL.md · MaxQuant + Perseus proteomics pipeline: run MaxQuant for LFQ and SILAC; parse proteinGroups.txt in Python; filter…

jaechang-hits/sciagent-skills · skills/proteomics-protein-engineering/metabolomics-workbench-database/SKILL.md · Query Metabolomics Workbench REST API (4,200+ NIH studies) for metabolite ID, study discovery, RefMet standardization…

jaechang-hits/sciagent-skills · skills/proteomics-protein-engineering/pride-database/SKILL.md · Search the PRIDE Archive v3 REST API for proteomics datasets: discover projects by keyword + faceted filters (organism…

jaechang-hits/sciagent-skills · skills/proteomics-protein-engineering/pyopenms-mass-spectrometry/SKILL.md · MS data processing with PyOpenMS for LC-MS/MS proteomics and metabolomics — mzML/mzXML I/O, signal processing…

jaechang-hits/sciagent-skills · skills/proteomics-protein-engineering/uniprot-protein-database/SKILL.md · Query UniProt REST API: search by gene/protein name, fetch FASTA, map IDs (Ensembl, PDB, RefSeq), access Swiss-Prot…

jaechang-hits/sciagent-skills · skills/scientific-computing/aeon/SKILL.md · scikit-learn compatible Python toolkit for time series ML: classify, cluster, regress, segment, transform with 30+…

jaechang-hits/sciagent-skills · skills/scientific-computing/astropy-astronomy/SKILL.md · Core Python library for astronomy/astrophysics: units with dimensional analysis, celestial coordinate transforms…

jaechang-hits/sciagent-skills · skills/scientific-computing/dask-parallel-computing/SKILL.md · Parallel/distributed computing for larger-than-RAM data. Components: DataFrames (parallel pandas), Arrays (parallel…

jaechang-hits/sciagent-skills · skills/scientific-computing/degenerate-input-filtering/SKILL.md · Filter degenerate, uninformative inputs before statistical tests: single-sequence alignments, empty files, constant…

jaechang-hits/sciagent-skills · skills/scientific-computing/exploratory-data-analysis/SKILL.md · Methodology for exploratory data analysis on scientific files. Decision frameworks by data type (tabular, sequence…

jaechang-hits/sciagent-skills · skills/scientific-computing/geopandas-geospatial/SKILL.md · Geospatial vector analysis extending pandas. Read/write spatial formats (Shapefile, GeoJSON, GeoPackage, Parquet…

jaechang-hits/sciagent-skills · skills/scientific-computing/hypogenic-hypothesis-generation/SKILL.md · LLM-driven hypothesis generation/testing on tabular data. Three methods: HypoGeniC (data-driven), HypoRefine…

jaechang-hits/sciagent-skills · skills/scientific-computing/matlab-scientific-computing/SKILL.md · MATLAB/GNU Octave numerical computing: matrices, linear algebra, ODEs, signal processing, optimization, statistics…

jaechang-hits/sciagent-skills · skills/scientific-computing/nan-safe-correlation/SKILL.md · Per-feature NaN-safe Spearman/Pearson correlation across many features (genes, proteins, variants) with missing values…

jaechang-hits/sciagent-skills · skills/scientific-computing/neb-irc-activation-energy/SKILL.md · NEB-IRC activation energy pipeline for reaction barriers using GFN2-xTB and pysisyphus. Optimize reactant and product…

jaechang-hits/sciagent-skills · skills/scientific-computing/networkx-graph-analysis/SKILL.md · Graph and network analysis toolkit. Four graph types (directed, undirected, multi-edge), centrality, shortest paths…

jaechang-hits/sciagent-skills · skills/scientific-computing/neurokit2/SKILL.md · Python toolkit for neurophysiological signal processing: ECG (HR, HRV, R-peaks), EEG (complexity, PSD), EMG (activation…

jaechang-hits/sciagent-skills · skills/scientific-computing/neuropixels-analysis/SKILL.md · Pipeline for Neuropixels extracellular electrophysiology: probe geometry (ProbeInterface), Kilosort sorting via…

jaechang-hits/sciagent-skills · skills/scientific-computing/nextflow-workflow-engine/SKILL.md · Dataflow workflow engine for scalable bioinformatics pipelines. Defines processes (containerized tasks) connected by…

jaechang-hits/sciagent-skills · skills/scientific-computing/polars-dataframes/SKILL.md · Fast in-memory DataFrame with lazy evaluation, parallel execution, Arrow backend. Use for tabular data in RAM (1–100…

jaechang-hits/sciagent-skills · skills/scientific-computing/pyhealth/SKILL.md · Python library for healthcare ML on EHR data: process MIMIC-III/IV, eICU, OMOP-CDM; encode medical codes (ICD, ATC…

jaechang-hits/sciagent-skills · skills/scientific-computing/pymatgen/SKILL.md · Python Materials Genomics library for structure analysis, thermodynamics, and electronic properties. Parse/create…

jaechang-hits/sciagent-skills · skills/scientific-computing/pymoo/SKILL.md · Python framework for single- and multi-objective optimization with evolutionary algorithms. Define vectorized…

jaechang-hits/sciagent-skills · skills/scientific-computing/scikit-learn-machine-learning/SKILL.md · Classical ML in Python: classification, regression, clustering, dim reduction, evaluation, tuning, preprocessing…

jaechang-hits/sciagent-skills · skills/scientific-computing/shap-model-explainability/SKILL.md · Model interpretability via SHAP (Shapley values from game theory). Covers explainer choice (Tree, Deep, Linear, Kernel…

jaechang-hits/sciagent-skills · skills/scientific-computing/simpy-discrete-event-simulation/SKILL.md · Process-based discrete-event simulation. Model queues, shared resources, timed events: manufacturing, service ops…

jaechang-hits/sciagent-skills · skills/scientific-computing/snakemake-workflow-engine/SKILL.md · Python-based workflow manager for reproducible, scalable pipelines. Define rules with file-based dependencies…

jaechang-hits/sciagent-skills · skills/scientific-computing/spikeinterface-electrophysiology/SKILL.md · Unified Python framework for extracellular electrophysiology. Load 20+ formats (SpikeGLX, OpenEphys, NWB, Intan…

jaechang-hits/sciagent-skills · skills/scientific-computing/sympy-symbolic-math/SKILL.md · Symbolic math in Python: exact algebra, calculus (derivatives, integrals, limits), equation solving, symbolic matrices…

jaechang-hits/sciagent-skills · skills/scientific-computing/torch-geometric-graph-neural-networks/SKILL.md · PyTorch Geometric (PyG) for graph neural networks: node/graph classification, link prediction with GCN, GAT, GraphSAGE…

jaechang-hits/sciagent-skills · skills/scientific-computing/transformers-bio-nlp/SKILL.md · HuggingFace Transformers with biomedical LMs (BioBERT, PubMedBERT, BioGPT, BioMedLM) for scientific NLP: NER (genes…

jaechang-hits/sciagent-skills · skills/scientific-computing/umap-learn/SKILL.md · UMAP dimensionality reduction for visualization, clustering prep, and feature engineering. Fast nonlinear manifold…

jaechang-hits/sciagent-skills · skills/scientific-computing/uspto-database/SKILL.md · Access USPTO patent data via PatentsView REST API and Google Patents Public Data (BigQuery). Search by inventor…

jaechang-hits/sciagent-skills · skills/scientific-computing/vaex-dataframes/SKILL.md · Out-of-core DataFrame for billion-row data via lazy evaluation and memory-mapped files. Use when data exceeds RAM (10…

jaechang-hits/sciagent-skills · skills/scientific-computing/zarr-python/SKILL.md · Chunked N-D arrays with compression and cloud storage. NumPy-style indexing. Backends: local, S3, GCS, ZIP, memory…

jaechang-hits/sciagent-skills · skills/scientific-writing/biorxiv-database/SKILL.md · Query bioRxiv/medRxiv preprints via REST API. Search by DOI, category, or date range; retrieve metadata (title…

jaechang-hits/sciagent-skills · skills/scientific-writing/cancer-research-figure-guide/SKILL.md · Cancer Research (AACR) figures: resolution (300-1200 DPI), formats (EPS/TIFF/AI), hierarchical panel labels (Ai, Aii…

jaechang-hits/sciagent-skills · skills/scientific-writing/cell-figure-guide/SKILL.md · Cell (Cell Press) figure preparation: resolution (300-1000 DPI), formats (TIFF/PDF), RGB color, Avenir/Arial fonts…

jaechang-hits/sciagent-skills · skills/scientific-writing/citation-management/SKILL.md · Selecting a reference manager and applying citation styles. Compares Zotero, Mendeley, EndNote, Paperpile; covers…

jaechang-hits/sciagent-skills · skills/scientific-writing/clinical-decision-support-documents/SKILL.md · Guidelines for clinical decision support (CDS) documents: biomarker-stratified cohort analyses and GRADE-graded…

jaechang-hits/sciagent-skills · skills/scientific-writing/elife-figure-guide/SKILL.md · eLife figure preparation: file formats (TIFF/EPS/PDF), striking image requirements (1800x900 px), figure supplement…

jaechang-hits/sciagent-skills · skills/scientific-writing/general-figure-guide/SKILL.md · Universal QA checklist for generated scientific plots: overlapping labels, clipped text, missing axes/legends…

jaechang-hits/sciagent-skills · skills/scientific-writing/hypothesis-generation/SKILL.md · Structured hypothesis formulation: turn observations into testable hypotheses with predictions, propose mechanisms…

jaechang-hits/sciagent-skills · skills/scientific-writing/lancet-figure-guide/SKILL.md · The Lancet figure preparation: resolution (300+ DPI at 120%), preferred editable formats (PowerPoint/Word/SVG), column…

jaechang-hits/sciagent-skills · skills/scientific-writing/latex-research-posters/SKILL.md · Research posters in LaTeX using beamerposter, tikzposter, or baposter. Layout, typography, color schemes, figure…

jaechang-hits/sciagent-skills · skills/scientific-writing/literature-review/SKILL.md · Conducting systematic, scoping, and narrative literature reviews. Covers PRISMA/PRISMA-ScR protocols, search strategy…

jaechang-hits/sciagent-skills · skills/scientific-writing/nature-figure-guide/SKILL.md · Nature figure preparation: resolution (300+ DPI), formats (AI/EPS/TIFF), RGB color, Helvetica/Arial fonts, lowercase…

jaechang-hits/sciagent-skills · skills/scientific-writing/nejm-figure-guide/SKILL.md · NEJM figure preparation: resolution (300-1200 DPI), editable vector formats (AI/EPS/SVG), in-house medical illustration…

jaechang-hits/sciagent-skills · skills/scientific-writing/openalex-database/SKILL.md · Query OpenAlex REST API for 250M+ scholarly works, authors, institutions, journals, concepts. Search by keyword…

jaechang-hits/sciagent-skills · skills/scientific-writing/peer-review-methodology/SKILL.md · Structured peer review of manuscripts and grants. 7-stage evaluation: initial assessment, section review, statistical…

jaechang-hits/sciagent-skills · skills/scientific-writing/pnas-figure-guide/SKILL.md · PNAS figure preparation: resolution (300-1000 PPI), formats (TIFF/EPS/PDF), strict RGB-only color, Arial/Helvetica…

jaechang-hits/sciagent-skills · skills/scientific-writing/pubmed-database/SKILL.md · Programmatic PubMed access via NCBI E-utilities REST API. Covers Boolean/MeSH queries, field-tagged search, endpoints…

jaechang-hits/sciagent-skills · skills/scientific-writing/science-figure-guide/SKILL.md · Science (AAAS) figure preparation: resolution (150-300+ DPI), formats (PDF/EPS/TIFF), RGB color, Myriad/Helvetica…

jaechang-hits/sciagent-skills · skills/scientific-writing/scientific-brainstorming/SKILL.md · Structured ideation methods: SCAMPER, Six Thinking Hats, Morphological Analysis, TRIZ, Biomimicry, plus more. Decision…

jaechang-hits/sciagent-skills · skills/scientific-writing/scientific-critical-thinking/SKILL.md · Evaluating scientific evidence and claims. Covers study design hierarchy (RCT to expert opinion), effect sizes (OR, RR…

jaechang-hits/sciagent-skills · skills/scientific-writing/scientific-literature-search/SKILL.md · Systematic strategies for searching scientific literature across PubMed, arXiv, Google Scholar, and AI-assisted tools…

jaechang-hits/sciagent-skills · skills/scientific-writing/scientific-manuscript-writing/SKILL.md · Scientific manuscript writing: IMRAD, citation styles (APA/AMA/Vancouver/IEEE), figures/tables, reporting guidelines…

jaechang-hits/sciagent-skills · skills/scientific-writing/scientific-schematics/SKILL.md · Designing scientific schematics, diagrams, and graphical abstracts. Covers tool selection (BioRender, Inkscape…

jaechang-hits/sciagent-skills · skills/scientific-writing/scientific-slides/SKILL.md · Scientific presentations for conferences, seminars, thesis defenses, and grant pitches. Slide design, talk structure…

jaechang-hits/sciagent-skills · skills/structural-biology-drug-discovery/aizynthfinder-retrosynthesis/SKILL.md · AiZynthFinder retrosynthetic route planning (CASP) from AstraZeneca Molecular AI. Monte Carlo tree search guided by a…

jaechang-hits/sciagent-skills · skills/structural-biology-drug-discovery/alphafold-database-access/SKILL.md · Access AlphaFold DB's 200M+ predicted structures by UniProt ID. Download PDB/mmCIF, analyze pLDDT/PAE, bulk-fetch…

jaechang-hits/sciagent-skills · skills/structural-biology-drug-discovery/autodock-vina-docking/SKILL.md · Molecular docking with AutoDock Vina (Python API). Receptor/ligand prep (Meeko + RDKit), grid box, docking, pose and…

jaechang-hits/sciagent-skills · skills/structural-biology-drug-discovery/chembl-database-bioactivity/SKILL.md · Query ChEMBL (2M+ compounds, 19M+ bioactivity measurements, 13K+ targets) via the public REST/JSON API with plain…

jaechang-hits/sciagent-skills · skills/structural-biology-drug-discovery/clinicaltrials-database-search/SKILL.md · Query ClinicalTrials.gov API v2 for trial data. Search by condition, drug/intervention, location, sponsor, or phase…

jaechang-hits/sciagent-skills · skills/structural-biology-drug-discovery/dailymed-database/SKILL.md · Query FDA drug labels (DailyMed) via REST API. Search structured product labels (SPLs) by name, NDC, set ID, or RxCUI…

jaechang-hits/sciagent-skills · skills/structural-biology-drug-discovery/datamol-cheminformatics/SKILL.md · Pythonic RDKit wrapper with sensible defaults for drug discovery. SMILES parsing, standardization, descriptors…

jaechang-hits/sciagent-skills · skills/structural-biology-drug-discovery/ddinter-database/SKILL.md · Query DDInter drug-drug interactions via REST API (1.7M+ interactions, 2,400+ drugs). Search by drug name/ID for…

jaechang-hits/sciagent-skills · skills/structural-biology-drug-discovery/deepchem/SKILL.md · Deep learning for drug discovery. 60+ models (GCN, GAT, AttentiveFP, MPNN, ChemBERTa, GROVER), 50+ featurizers…

jaechang-hits/sciagent-skills · skills/structural-biology-drug-discovery/diffdock/SKILL.md · Diffusion-based docking that predicts protein-ligand poses without a predefined site. Use for blind docking, when…

jaechang-hits/sciagent-skills · skills/structural-biology-drug-discovery/drugbank-database-access/SKILL.md · Parse local DrugBank XML for drug info, interactions, targets, and properties. Search by ID/name/CAS, extract DDIs with…

jaechang-hits/sciagent-skills · skills/structural-biology-drug-discovery/emdb-database/SKILL.md · Look up EMDB cryo-EM density maps and fitted atomic models via the entry REST API + EBI Search WS. Fetch entry metadata…

jaechang-hits/sciagent-skills · skills/structural-biology-drug-discovery/fda-database/SKILL.md · Query openFDA REST API for adverse events (FAERS), labeling, product info, recalls, enforcement. Search by drug name…

jaechang-hits/sciagent-skills · skills/structural-biology-drug-discovery/gtopdb-database/SKILL.md · Query IUPHAR/BPS Guide to Pharmacology (GtoPdb) for receptor-ligand interactions, target/ligand metadata, families, and…

jaechang-hits/sciagent-skills · skills/structural-biology-drug-discovery/mdanalysis-trajectory/SKILL.md · Analyze MD trajectories from GROMACS, AMBER, NAMD, CHARMM, LAMMPS. Reads topology/trajectory into Universe objects…

jaechang-hits/sciagent-skills · skills/structural-biology-drug-discovery/mdtraj-trajectory-analysis/SKILL.md · mdtraj molecular dynamics trajectory analysis (Python). Reads DCD/XTC/TRR/NetCDF/H5/PDB topologies and trajectories…

jaechang-hits/sciagent-skills · skills/structural-biology-drug-discovery/medchem/SKILL.md · Medicinal chemistry filters for compound triage. Drug-likeness rules (Lipinski Ro5, Veber, Oprea, CNS, leadlike, REOS…

jaechang-hits/sciagent-skills · skills/structural-biology-drug-discovery/molfeat-molecular-featurization/SKILL.md · Molecular featurization hub (100+ featurizers) for ML. SMILES to fingerprints (ECFP, MACCS, MAP4), descriptors (RDKit…

jaechang-hits/sciagent-skills · skills/structural-biology-drug-discovery/opentargets-database/SKILL.md · Query Open Targets GraphQL API for target-disease associations, evidence, drug links, safety. Search targets by gene…

jaechang-hits/sciagent-skills · skills/structural-biology-drug-discovery/pdb-database/SKILL.md · Query RCSB PDB (200K+ structures) via the public REST + GraphQL APIs with plain `requests` (no SDK). Search by text…

jaechang-hits/sciagent-skills · skills/structural-biology-drug-discovery/pubchem-compound-search/SKILL.md · Query PubChem (110M+ compounds) directly via the PUG-REST/JSON API with plain `requests` — no SDK install required…

jaechang-hits/sciagent-skills · skills/structural-biology-drug-discovery/pytdc-therapeutics-data-commons/SKILL.md · Therapeutics Data Commons (TDC) AI-ready drug discovery datasets. Curated ADME, toxicity, DTI, DDI with scaffold/cold…

jaechang-hits/sciagent-skills · skills/structural-biology-drug-discovery/rdkit-chemdraw-cdxml/SKILL.md · Read, write, and edit ChemDraw CDX/CDXML files with RDKit's rdkit.Chem.rdChemDraw plus direct XML editing, always…

jaechang-hits/sciagent-skills · skills/structural-biology-drug-discovery/rdkit-cheminformatics/SKILL.md · Cheminformatics toolkit for molecular analysis and virtual screening: SMILES/SDF parsing, descriptors (MW, LogP, TPSA)…

jaechang-hits/sciagent-skills · skills/structural-biology-drug-discovery/rowan/SKILL.md · Cloud quantum chemistry platform with Python SDK. Run geometry optimization, conformer generation, torsional scans, and…

jaechang-hits/sciagent-skills · skills/structural-biology-drug-discovery/sar-analysis/SKILL.md · Structure-activity relationship (SAR) analysis guide for drug discovery including molecular descriptor analysis…

jaechang-hits/sciagent-skills · skills/structural-biology-drug-discovery/smina-molecular-docking/SKILL.md · smina molecular docking CLI. AutoDock Vina fork with customizable scoring functions, native SDF/MOL2/PDB ligand input…

jaechang-hits/sciagent-skills · skills/structural-biology-drug-discovery/torchdrug/SKILL.md · PyTorch-based ML platform for drug discovery: graph molecular representation learning, property prediction (ADMET…

jaechang-hits/sciagent-skills · skills/structural-biology-drug-discovery/unichem-database/SKILL.md · Cross-reference compound IDs across 20+ databases (ChEMBL, DrugBank, PubChem, ChEBI, PDB, SureChEMBL, HMDB…

jaechang-hits/sciagent-skills · skills/structural-biology-drug-discovery/zinc-database/SKILL.md · Query the ZINC22 virtual compound library (CartBlanche API, billions of make-on-demand + purchasable molecules). Look…