Research & Science · Bioinformatics

Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats.

spacering-net/codeg

Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API.

google-deepmind/science-skills

Estimates reaction fluxes inside cells from steady-state carbon-13 labeling data with a bundled mfapy-based solver, and reports which fluxes the data pin down.

K-Dense-AI/scientific-agent-skills

A skill your agent uses when needing clinical significance, pathogenicity classifications (e.g., Pathogenic, Benign, VUS), clinical evidence rationales, or finding "hard positive" benchmark controls…

google-deepmind/science-skills

Turns a broad metabolic modelling topic into a concrete, paper-shaped plan with organism, model, perturbations, metrics and figures before any FBA code is written.

aiming-lab/AutoResearchClaw

A skill your agent uses when you want to look up, map, and search for short genetic variants (SNPs, indels) in NCBI's dbSNP database.

google-deepmind/science-skills

Runs a metabolic flux analysis from model loading to phenotype prediction and figures by handing work to four sub-agents in sequence.

aiming-lab/AutoResearchClaw

A skill your agent uses when designing, reviewing, or implementing single-cell RNA-seq QC in Python or R with a human-in-the-loop, data-driven approach.

xuzhougeng/wisp-science

Performs quality control on single-cell RNA-seq data (.h5ad or .h5 files) using scverse best practices with MAD-based filtering and comprehensive visualizations.

FreedomIntelligence/OpenClaw-Medical-Skills

Query the Genome Aggregation Database (gnomAD). An agent skill from google-deepmind/science-skills.

google-deepmind/science-skills

Generate a specialized domain-expert research agent modeled on PaperClaw architecture.

guhaohao0991/PaperClaw

Predict genome-wide functional tracks (RNA-seq, CAGE, DNase, ChIP) from DNA sequence with Borzoi.

JimLiu/science-skills

Routes bioinformatics, drug discovery, clinical and multi-omics tasks from a chat interface to Claude Code sessions running K-Dense scientific skills, with a live dashboard per task.

xjtulyc/MedgeClaw

A skill your agent uses for genetics, genome source, variant, gene, phenotype, disease, screen, pharmacogenomics, and Genomi install/setup maintenance questions.

exon-research/genomi

Routes agents to the right tangermeme reference for analyzing trained genomic deep learning models, from attributions and motif experiments to variant effects and design.

jmschrei/tangermeme

Analyze single-cell data with core Scarf, the out-of-core Zarr DataStore library with immutable artifacts and pipeline runs.

NygenAnalytics/scarf

A skill your agent uses when the user asks about TBtools, TBtools-II, TBtools RPC API, TBtools CLI, or bioinformatics operations available through TBtools such as sequence manipulation, BLAST…

xuzhougeng/wispterm

Route NVIDIA Parabricks pbrun tools, assess GPU/runtime readiness, and provide version-aware command guidance for FASTQ/BAM processing, RNA-seq, variant calling, BAM QC, and GVCF workflows.

NVIDIA-BioNeMo/bionemo-agent-toolkit

Run SnpEff, a variant annotation and effect prediction tool for genomic variants.

pcingola/SnpEff

Builds or loads a genome-scale metabolic model in COBRApy, sets its growth medium and objective, and exports it as a validated JSON file for flux analysis.

aiming-lab/AutoResearchClaw

Score, embed, and generate DNA sequences with Evo 2, a long-context genomic foundation model.

JimLiu/science-skills

Generate sashimi-style genome visualization plots (coverage, line, heatmap, IGV read-by-read, HiC, circRNA, motif) from BAM/bigWig/depth/HiC inputs.

ygidtu/trackplot

Auto-activate when the user mentions NGLess, ngless, NGS processing, metagenomics pipelines with NGLess, writing .ngl scripts, or is working in the ngless repository (Rust source at src/).

ngless-toolkit/ngless

A skill your agent uses when a researcher needs to query biomedical databases for biomarker discovery, build target profiles from UniProt/Open Targets/STRING, rank biomarker candidates by evidence…

aws-samples/amazon-bedrock-agents-healthcare-lifesciences

jujutsu (jj) command cheatsheet for this colocated jj+git Bioconductor repo.

seandavi/GEOquery

Run flexynesis, a deep-learning suite for multi-omics data integration and clinical outcome prediction (drug response, cancer subtyping, survival analysis).

BIMSBbioinfo/flexynesis

Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO.

GPTomics/bioSkills

Generate Amazon and cross-border ecommerce product images from a product business card.

binggandata/bggg-skills

Installs the bioSkills collection of 425 bioinformatics skills in one step, or only chosen categories, so sequencing, RNA-seq, single-cell and variant tasks get specialized help.

GPTomics/bioSkills

A skill your agent uses when interpreting genomic variants from VCF files, performing clinical variant classification using ClinVar/VEP annotations, analyzing allele frequencies against population…

aws-samples/amazon-bedrock-agents-healthcare-lifesciences

Quick reference for Biopython work: sequence operations, SeqIO file parsing, BLAST searches, Entrez queries, phylogenetic trees and PDB structure analysis.

aiming-lab/AutoResearchClaw

Workflow for fixing or changing RNAlysis code that talks to an EXTERNAL WEB SERVICE — UniProt, Ensembl, PANTHER, PhylomeDB, OrthoInspector, KEGG, or GO.

GuyTeichman/RNAlysis

Queries the UniProt REST API directly to search proteins, fetch FASTA sequences, map IDs between databases and read Swiss-Prot and TrEMBL entries.

davila7/claude-code-templates

Write biological sequences to files (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO.

GPTomics/bioSkills

A skill your agent uses when a developer wants to build a new healthcare or life sciences agent, structure tools and system prompts for an HCLS workflow, or create a Strands agent with…

aws-samples/amazon-bedrock-agents-healthcare-lifesciences

Run AlphaGenome-PyTorch to get genomic track predictions — via the agt predict CLI (single locus, BED regions, whole chromosomes, raw FASTA sequences, or per-gene count tables/AnnData), variant…

genomicsxai/alphagenome-pytorch

Walks through single-cell RNA-seq analysis with Scanpy: loading .h5ad and 10X data, QC, normalization, PCA and UMAP, Leiden clustering, marker genes and cell type annotation.

davila7/claude-code-templates

Capture and attach RNAlysis GUI screenshots to a PR whenever a change makes a VISIBLE difference to a GUI dialog.

GuyTeichman/RNAlysis

Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3).

davila7/claude-code-templates

Embed and annotate single-cell expression data with scGPT, a foundation model for single-cell biology.

JimLiu/science-skills

Run or continue patient-authorized, genome-informed GenomiLab investigations in the current Claude, Codex, or other MCP agent task.

exon-research/genomi

Implements a new bioinformatics tool wrapper in proto-tools using a parallelized agent pipeline.

evo-design/proto-tools

End-to-end 10x Visium spatial transcriptomics analysis workflow with staged execution and human review gates.

QING1105/ezST

Reproducible Scanpy workflow for human or mouse 10x scRNA-seq and snRNA-seq count matrices: single-sample descriptive QC, clustering and annotation, or comparative donor-aware pseudobulk DE and Milo…

PKU-YuanGroup/OpenAI4S

Load when the user needs Deterministic fixed-period 24-hour single-component cosinor OLS rhythm analysis for a bulk RNA time-course CSV.

TianGzlab/OmicsClaw

Guides use of deepTools on sequencing data: BAM to bigWig conversion, QC, sample correlation, and heatmaps or profiles around TSS and peaks for ChIP-seq, RNA-seq and ATAC-seq.

davila7/claude-code-templates

Runs flux balance analysis and related constraint-based simulations on a COBRApy metabolic model, from standard FBA to gene knockouts and carbon source swaps.

aiming-lab/AutoResearchClaw

Make RNAlysis code faster while proving the output does not change.

GuyTeichman/RNAlysis