jaechang-hits/sciagent-skills
57 skills · 1,794 total installs
$npx skills add jaechang-hits/sciagent-skillsSkillInstalls
matplotlib-scientific-plottingLow-level Python plotting for scientific figures: publication-quality line, scatter, bar, heatmap, contour, 3D; multi-panel layouts; fine control of every…biopython-molecular-biologyMolecular biology toolkit: sequence manipulation, FASTA/GenBank/PDB I/O, NCBI Entrez, BLAST automation, pairwise/MSA alignment, Bio.PDB, phylogenetic trees.biopython-sequence-analysisBiopython sequence analysis: parse FASTA/FASTQ/GenBank/GFF (SeqIO), NCBI Entrez (esearch/efetch/elink), remote/local BLAST, pairwise/MSA alignment…cellpose-cell-segmentationDL cell/nucleus segmentation for fluorescence and brightfield microscopy.napari-image-viewerInteractive viewer for microscopy. Displays 2D/3D/4D arrays as Image, Labels, Points, Shapes, Tracks layers; supports annotation, plugin analysis, headless…statistical-analysisGuided statistical analysis: test choice, assumption checks, effect sizes, power, APA reporting.pymc-bayesian-modelingBayesian modeling with PyMC 5: priors, likelihood, NUTS/ADVI sampling, diagnostics (R-hat, ESS), LOO/WAIC comparison, prediction.opencv-bioimage-analysisComputer vision for bio-image preprocessing, feature detection, real-time microscopy.pyimagej-fiji-bridgePython bridge to ImageJ2/Fiji for macros, plugins (Bio-Formats, TrackMate, Analyze Particles), NumPy↔ImagePlus/ImgLib2 exchange, and ImageJ Ops.scientific-visualizationGuide for choosing and creating scientific visualizations for publications and talks.scikit-survival-analysisTime-to-event modeling with scikit-survival: Cox PH (elastic net), Random Survival Forests, Boosting, SVMs for censored data.seaborn-statistical-plotsStatistical visualization on matplotlib with native pandas support.plotly-interactive-plotsInteractive scientific visualization with Plotly. Two APIs: plotly.express (px) for one-liner DataFrame plots, plotly.graph_objects (go) for trace-level…statsmodels-statistical-modelingPython statistical modeling: regression (OLS, WLS, GLM), discrete (Logit, Poisson, NegBin), time series (ARIMA, SARIMAX, VAR), with rigorous inference,…arboreto-grn-inferenceGRN inference from expression via GRNBoost2 (gradient boosting) or GENIE3 (Random Forest).etetoolkitETE Toolkit (ETE3): Python phylogenetic tree analysis and visualization.flowio-flow-cytometryParse/write FCS (Flow Cytometry) files v2.0-3.1. Events as NumPy, channel metadata, multi-dataset files, CSV/FCS export. Use FlowKit for gating/compensation.scikit-image-processingPython image processing for microscopy and bioimage analysis. Read/write images, filter (Gaussian, median, LoG), segment (thresholding, watershed, active…statistical-significance-annotationGuide for annotating statistical significance (p-value asterisks) on comparison plots.homer-motif-analysisDe novo and known TF motif enrichment in ChIP-seq/ATAC-seq peaks via HOMER.trackpy-particle-trackingPython library for single-particle tracking (SPT) in video microscopy via the Crocker-Grier algorithm.sciagent-skill-creatorScaffold a new SciAgent-Skills entry. Picks pipeline/toolkit/database/guide template, creates skills/{category}/{name}/SKILL.md with valid frontmatter, appends…archs4-databaseQuery ARCHS4 REST API for uniformly processed RNA-seq expression, tissue patterns, co-expression across 1M+ human/mouse samples.gene-databaseNCBI Gene via E-utilities: curated records across 1M+ taxa. Official symbols, aliases, RefSeq IDs, summaries, coordinates, GO, interactions.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.clinpgx-databaseQuery the ClinPGx (formerly PharmGKB) REST API plus the CPIC PostgREST companion API for pharmacogenomic clinical annotations, CPIC/DPWG dosing guidelines,…dbsnp-databaseQuery NCBI dbSNP for SNP records by rsID, gene, or region via E-utilities and Variation Services REST API.geo-databaseNCBI GEO access via GEOparse and E-utilities. Search by keyword/organism/platform, download GSE series matrices, parse GPL annotations, extract GSM metadata,…monarch-databaseMonarch Initiative knowledge graph REST API for disease-gene-phenotype associations and cross-species orthology.samtools-bam-processingCLI toolkit for SAM/BAM/CRAM: sort, index, convert, filter, QC alignments. Core commands: view, sort, index, flagstat, stats, depth, markdup, merge.bioservices-multi-databaseUnified Python interface to 40+ bioinformatics web services: UniProt proteins, KEGG pathways, ChEMBL/ChEBI/PubChem, BLAST, cross-database ID mapping, GO…cbioportal-databaseCancer genomics (TCGA et al.) via cBioPortal REST API. Retrieve somatic mutations, CNAs, expression, clinical data (survival/stage/treatment) across thousands…clinvar-databaseQuery NCBI ClinVar via E-utilities for variant clinical significance, pathogenicity, disease associations.cosmic-databaseQuery COSMIC for cancer somatic mutations, gene census, mutational signatures, drug resistance variants.ena-databaseENA REST API for sequences, reads, assemblies, and annotations.encode-databaseENCODE Portal REST API for regulatory genomics: TF ChIP-seq, ATAC-seq/DNase-seq peaks, histone marks, and RNA-seq across 1000+ cell types.ensembl-databaseEnsembl REST API for gene/transcript/variant annotations in 300+ species.gget-genomic-databasesUnified CLI/Python interface to 20+ genomic databases. Gene lookups (Ensembl search/info/seq), BLAST/BLAT, AlphaFold, Enrichr enrichment, OpenTargets…gnomad-databasegnomAD v4 population variant frequencies via GraphQL API. Allele counts and frequencies stratified by ancestry (AFR, AMR, EAS, NFE, SAS, FIN, ASJ, MID),…gwas-databaseNHGRI-EBI GWAS Catalog REST API for SNP-trait associations from published GWAS. Query studies, associations, variants, traits, genes, summary stats.jaspar-databaseJASPAR 2024 TF binding profiles via REST API and pyJASPAR. Retrieve PFMs/PWMs by TF name, JASPAR ID, species, or structural class.kegg-databaseKEGG REST API (academic only). Pathways, genes, compounds, enzymes, diseases, drugs via 7 ops (info/list/find/get/conv/link/ddi).mouse-phenome-databaseRetrieve mouse phenotype data from the Jackson Laboratory Mouse Phenome Database (MPD) via its REST API.opentrons-integrationOpentrons Protocol API v2 for OT-2/Flex: Python protocols for pipetting, serial dilutions, PCR, plate replication; control thermocycler, heater-shaker,…plotly-interactive-visualizationprokka-genome-annotationAnnotate prokaryotic genomes (bacteria, archaea, viruses) via Prokka's BLAST/HMM pipeline.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.quickgo-databaseQuery EBI QuickGO REST API for GO terms and protein annotations.regulomedb-databaseQuery RegulomeDB v2 GET REST API to score variants for regulatory function and retrieve overlapping evidence (TF binding, histone marks, DNase peaks,…remap-databaseQuery ReMap 2022 TF ChIP-seq peak database via REST API and BED downloads.seaborn-statistical-visualizationStatistical visualization on matplotlib + pandas. Distributions (histplot, kdeplot, violin, box), relational (scatter, line), categorical, regression,…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.ucsc-genome-browserQuery UCSC Genome Browser REST API for DNA sequences, tracks, gene models, and conservation across 100+ assemblies.depmap-crispr-essentialityDepMap CRISPR gene effect (Chronos) analysis: sign convention for essentiality, per-gene NaN-safe Spearman correlation, data loading/alignment.single-cell-annotationBest practices for single-cell RNA-seq cell type annotation including marker-based, reference-based, and automated classification approaches.bakta-genome-annotationAnnotate bacterial and archaeal genomes and plasmids with Bakta's Prodigal/HMM/diamond pipeline.roary-pangenomeCompute the bacterial pan-genome from Prokka/Bakta GFF3 annotations with Roary's CD-HIT + BLAST + MCL clustering pipeline.