Research & Science · For data scientists

Trains and applies base-resolution deep learning models on ChIP-seq / ChIP-nexus / CUT&RUN data.

GPTomics/bioSkills

A skill your agent uses when a paper needs publication-ready figures or a visual abstract.

Aperivue/medsci-skills

Inspect and audit GEPA genomes via the @metaharness/darwin/gepa library entry (darwin 0.8.0) — load/validate a genome (default is the shipped cand-6 promotion), render the system prompt a genome…

ruvnet/ruflo

基于东方财富数据库，支持自然语言搜索全网最新公告、研报、财经新闻、交易所动态及官方政策等，覆盖全球市场标的，可用于热点捕捉、舆情监控、研报速览、公告精读及投资决策等场景。Natural language search for financial information, covering authoritative sources including news, announcements…

hiboys/ExploreFinance

Process multiple sequence files in batch using Biopython. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills.

FreedomIntelligence/OpenClaw-Medical-Skills

Polish assemblies and call variants from Oxford Nanopore data using medaka.

FreedomIntelligence/OpenClaw-Medical-Skills

Preprocessing and harmonization of multi-omics data before integration.

FreedomIntelligence/OpenClaw-Medical-Skills

Analyze time-series RNA-seq data using limma voom with splines, maSigPro, and ImpulseDE2.

FreedomIntelligence/OpenClaw-Medical-Skills

Quality control and assessment for proteomics data. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills.

FreedomIntelligence/OpenClaw-Medical-Skills

Compute spatial statistics for spatial transcriptomics data using Squidpy.

FreedomIntelligence/OpenClaw-Medical-Skills

Extract per-molecule embeddings from any encoder-bearing KERMT checkpoint (groverbase / cmim / hybrid / finetuned).

NVIDIA-BioNeMo/bionemo-agent-toolkit

Computes and interprets treatment effect measures (OR, RR, RD, HR, NNT) with calibrated confidence intervals (Wilson, Newcombe, Miettinen-Nurminen, MOVER, profile likelihood, Bender NNT) and reports…

GPTomics/bioSkills

Build volcano and MA plots from differential-expression / association results with LFC shrinkage, FDR-adjusted thresholds, sensible label placement, and axis-truncation conventions.

GPTomics/bioSkills

Predicts whether a DNA variant alters mRNA splicing using sequence-based deep-learning tools — SpliceAI (10kb context dilated CNN, clinical default), Pangolin (multi-tissue), MMSplice (modular…

GPTomics/bioSkills

Automated sequencing quality control and advanced visualization wrapping FastQC, MultiQC, and custom chart generation.

ClawBio/ClawBio

Formal mathematical reasoning for research papers — derive equations, write proofs, formalize problem settings, select statistical tests, and generate LaTeX math notation.

lingzhi227/agent-research-skills

A skill your agent uses when the user wants academic writing prompts, paper polishing workflows, translation/rewrite guidance, reviewer-style paper critique, experiment write-up help, title/caption…

Citrus-bit/Anaxa

A skill your agent uses when cleaning clinical trial data, preparing data for FDA/EMA submission, standardizing SDTM datasets, handling missing values in clinical studies, detecting outliers in lab…

aipoch/medical-research-skills

A skill your agent uses when evaluating the clinical utility of a binary prediction model from a single clinical CSV file by fitting a logistic decision-curve model, plotting decision and…

aipoch/medical-research-skills

Programmatic access to DrugBank drug and target data; use when you need to download, parse, and analyze DrugBank XML for properties, interactions, pathways, and pharmacology.

aipoch/medical-research-skills

ETE (Environment for Tree Exploration) toolkit for phylogenetic and hierarchical tree analysis; use it when you need to parse/manipulate Newick/NHX trees, detect duplication/speciation events…

aipoch/medical-research-skills

Generates a Meta-analysis results section description for funnel plots, including statistical tables (Egger's, Begg's, Trim & Fill) and figure legends.

aipoch/medical-research-skills

Differential gene expression analysis for bulk RNA-seq count matrices using a DESeq2-like workflow in Python; use when you need Wald tests, FDR correction, and optional LFC shrinkage for…

aipoch/medical-research-skills

Comprehensive tool for computational mass spectrometry using PyOpenMS; use when you need to read/write MS formats (mzML/mzXML/MGF), run signal processing (smoothing/peak picking), detect isotope…

aipoch/medical-research-skills

Therapeutics Data Commons (PyTDC) for AI-ready therapeutic ML datasets and benchmarks; use it when you need standardized dataset loading, meaningful splits (e.g., scaffold/cold-start), and…

aipoch/medical-research-skills

Parses, queries, converts, and extracts from GTF and GFF3 gene-model annotation files - walking the gene/transcript/exon/CDS hierarchy with gffutils (queryable SQLite DB), converting formats and…

GPTomics/bioSkills

Maps query single-cell data onto reference atlases and transfers cell-type labels using scArches surgery (scVI/scANVI), Symphony, Azimuth, CellTypist, scPoli, popV, and foundation models, with…

GPTomics/bioSkills

Designs QC, corrects signal drift, removes batch effects, filters features, normalizes samples, and imputes missing values for untargeted LC-MS/GC-MS metabolomics, framing each step as a measurement…

GPTomics/bioSkills

Turns a shotgun profiler table (MetaPhlAn relative abundance, Bracken counts, HUMAnN function tables) into honest figures and defensible community statistics with phyloseq, vegan, microViz, and…

GPTomics/bioSkills

Turns raw Illumina Infinium methylation BeadChip IDATs (450K, EPIC, EPICv2) into a defensible beta/M matrix with sesame (openSesame/SigDF) or minfi (RGChannelSet - MethylSet - GenomicRatioSet).

GPTomics/bioSkills

Stratifies patients into multi-omics subtypes by building one patient-by-patient similarity network per omic, fusing them with SNF's cross-network diffusion, and spectral-clustering the fused graph…

GPTomics/bioSkills

Exports publication-ready figures with the correct vector/raster split, embedded editable fonts, color-space-robust palettes, and journal-correct sizing and resolution in matplotlib and ggplot2.

GPTomics/bioSkills

Calculate assembly and sequence statistics (N50/L50, auN, NG50/NGA50, length distribution, GC content with ambiguity handling, summary reports) using Biopython.

GPTomics/bioSkills

Detects spatially variable genes, spatial autocorrelation, and cell-type colocalization for spatial transcriptomics using Squidpy with PySAL/esda for local statistics.

GPTomics/bioSkills

Compute and interpret VCF quality-control metrics (Ti/Tv, het/hom, novel/known, missingness, HWE, contamination, relatedness) with bcftools stats, vcftools, plot-vcfstats, and identity tools…

GPTomics/bioSkills

Orchestrates the end-to-end bisulfite/EM-seq methylation pipeline from FASTQ to differentially methylated regions, chaining Trim Galore/fastp QC, Bismark alignment + deduplication, methylation…

GPTomics/bioSkills

Orchestrates neoantigen discovery from somatic variants to ranked vaccine candidates, chaining HLA typing (OptiType/arcasHLA + LOHHLA), VEP annotation (Wildtype+Frameshift plugins) +…

GPTomics/bioSkills

This skill covers Bayesian estimation and inference in quantitative social science.

brycewang-stanford/Auto-Empirical-Research-Skills

Industrial AI literature research with mandatory intake questions, venue-aware source prioritization, structured report outputs, and survey draft generation.

brycewang-stanford/Auto-Empirical-Research-Skills

Fast high-dimensional fixed effects: OLS, Poisson, IV with multi-way FE; DiD (TWFE, did2s, Sun-Abraham); clustered SEs; etable/coefplot/iplot.

brycewang-stanford/Auto-Empirical-Research-Skills

Econometrics skill for machine learning methods in causal inference.

brycewang-stanford/Auto-Empirical-Research-Skills

Interpret completed experimental outputs after host/runtime execution using pre-declared statistical tests, effect/uncertainty estimates, reproducibility checks, and calibrated synthesis.

yogsoth-ai/de-anthropocentric-research-engine

A skill your agent uses when the user is planning a two-arm comparison (an A/B test, a simple RCT, a behavioral study, or a two-model/two-config evaluation) and needs to size it and preregister it…

gaasher/Agent-Loop-Skills

Analyzes forest plots for meta-analysis, generating detailed descriptions and formatting figure legends in Chinese or English.

aipoch/medical-research-skills

Generates the "Risk of Bias" results section for a meta-analysis based on assessment tables and statistics.

aipoch/medical-research-skills

Operates the QIIME2 framework as the glue for an amplicon analysis - the .qza/.qzv artifact model, semantic types (FeatureTable[Frequency], SampleData[PairedEndSequencesWithQuality]…

GPTomics/bioSkills

Scans genomes for natural selection with SFS tests (Tajima's D, Fay & Wu H, Zeng E, SweepFinder2 CLR), haplotype tests (iHS, nSL, XP-EHH, Rsb, H12), and differentiation (FST, PBS) using…

GPTomics/bioSkills

Tests for differentially abundant proteins between conditions with limma/DEqMS empirical-Bayes moderation, proDA/msqrob2/MSstats missingness modeling, and Python Welch+BH alternatives.

GPTomics/bioSkills