Research & Science · Embeddings

Biohub ESMFold2 / ESMFold2-Fast all-atom co-folding (Candido et al.

JimLiu/science-skills

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

JimLiu/science-skills

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

JimLiu/science-skills

This skill should be used when working with genomic interval data (BED files) for machine learning tasks.

davila7/claude-code-templates

A skill your agent uses when the user wants to survey a journal or field, fetch papers from OpenAlex, cluster topics, build exploration embeddings, or search named explore libraries under…

ZimoLiao/scholaraio

Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and…

davila7/claude-code-templates

A standardized CLI wrapper for Uni-Mol molecular ML workflows that handles representation extraction (embeddings), model training (regression/classification), and property prediction with built-in…

jinzhezenggroup/computational-chemistry-agent-skills

Semantic Similarity Index for disease research literature using PubMedBERT embeddings

ClawBio/ClawBio

Write code that calls the installed nvMolKit Python API for GPU-accelerated, batched RDKit-style operations - Morgan fingerprints, Tanimoto/cosine similarity, ETKDG conformer embedding, MMFF/UFF…

NVIDIA-BioNeMo/bionemo-agent-toolkit

Design and analyze studies in sociolinguistics, language variation, acoustic phonetics, discourse analysis, language contact, and computational linguistics.

joshzyj/open-scholar-skill

Semantic search across UK Biobank's 12,000+ data fields and publications — find the right variables for your research question.

ClawBio/ClawBio

Featurizes small molecules with Molfeat for QSAR/QSPR, chemical similarity, virtual screening, and molecular ML.

K-Dense-AI/scientific-agent-skills

Local scVI/scANVI-based single-cell latent embedding and batch-aware integration from raw-count .h5ad or 10x Matrix Market input, with stable integrated AnnData export for downstream latent analysis.

ClawBio/ClawBio

Produce and interpret PCA, t-SNE, UMAP, and PHATE plots for high-dimensional omics data with rigor about which method preserves what (variance, local structure, manifold, transitions)…

GPTomics/bioSkills

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

NVIDIA-BioNeMo/bionemo-agent-toolkit

Given a gene and a single-cell atlas, compute how cell-type-specific its expression is — the tau specificity index, Sarle's expression bimodality coefficient, and the cell types that drive the…

ClawBio/ClawBio

A skill your agent uses when performing sample-level dimensionality reduction and visualization on abundance or OTU-style matrices with a companion group file, generating UMAP and/or t-SNE…

aipoch/medical-research-skills

Integrate multimodal single-cell data (CITE-seq RNA+protein, 10x Multiome RNA+ATAC, unpaired/diagonal RNA+ATAC) and choose the right joint method.

GPTomics/bioSkills

Orchestrates the end-to-end 10x Multiome (paired scRNA + scATAC) pipeline from Cell Ranger ARC output to a jointly-embedded, annotated object, chaining per-modality QC, AMULET fragment-based ATAC…

GPTomics/bioSkills

Walk through omicverse's single-cell preprocessing tutorials to QC PBMC3k data, normalise counts, detect HVGs, and run PCA/embedding pipelines on CPU, CPU–GPU mixed, or GPU stacks.

FreedomIntelligence/OpenClaw-Medical-Skills

Molecular featurization hub (100+ featurizers) for ML. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

Machine learning toolkit for genomic interval (BED) data; use it when you need to tokenize BED collections and train embeddings for regions/cells/labels, build consensus peak universes, or run…

aipoch/medical-research-skills

Toolkit for protein language models (ESM3 for multimodal generative protein design; ESM C for efficient embeddings).

aipoch/medical-research-skills

Implement open science practices for a social science study.

joshzyj/open-scholar-skill

Load when building the neighbour graph, embedding (UMAP/t-SNE/diffmap/PHATE), and clustering (Leiden/Louvain) on a normalised single-cell AnnData.

TianGzlab/OmicsClaw

Load when aggregating single cells into metacells (sample-aware coarse-grained pseudo-cells) on a normalised scRNA AnnData via SEACells or KMeans on a low-D embedding.

TianGzlab/OmicsClaw

Protein language models (ESM3, ESM C) for sequence generation, structure prediction, inverse folding, and embeddings.

jaechang-hits/SciAgent-Skills

ESM2 protein language model for embeddings and sequence scoring.

NeverSight/learn-skills.dev

Python library for genomic interval ML. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills