Skill · em Dados, IA e pesquisa

geniml

This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for training region embeddings (Region2Vec, BEDspace), single-cell ATAC-seq analysis (scEmbed), building consensus peaks (universes), or any ML-based analysis of genomic regions. Applies to…

Procedência

Antes de instalar

6 arquivos · 36,1 KB · só texto, nenhum script

Instalar na sua CLI

O comando baixa a versão fixada (commit 57f899e) direto da origem, para a pasta que a CLI lê. Precisa de curl (macOS e Linux); no Windows não há comando, porque o Rook Labs é para macOS.

Claude Code

Neste projeto: instala em .claude/skills/geniml/.

d=".claude/skills/geniml"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/geniml"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/bedspace.md" "$u/references/bedspace.md" \
  -o "$d/references/consensus_peaks.md" "$u/references/consensus_peaks.md" \
  -o "$d/references/region2vec.md" "$u/references/region2vec.md" \
  -o "$d/references/scembed.md" "$u/references/scembed.md" \
  -o "$d/references/utilities.md" "$u/references/utilities.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Global: instala em ~/.claude/skills/geniml/.

d="$HOME/.claude/skills/geniml"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/geniml"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/bedspace.md" "$u/references/bedspace.md" \
  -o "$d/references/consensus_peaks.md" "$u/references/consensus_peaks.md" \
  -o "$d/references/region2vec.md" "$u/references/region2vec.md" \
  -o "$d/references/scembed.md" "$u/references/scembed.md" \
  -o "$d/references/utilities.md" "$u/references/utilities.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Codex

Neste projeto: instala em .agents/skills/geniml/.

d=".agents/skills/geniml"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/geniml"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/bedspace.md" "$u/references/bedspace.md" \
  -o "$d/references/consensus_peaks.md" "$u/references/consensus_peaks.md" \
  -o "$d/references/region2vec.md" "$u/references/region2vec.md" \
  -o "$d/references/scembed.md" "$u/references/scembed.md" \
  -o "$d/references/utilities.md" "$u/references/utilities.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Global: instala em ~/.agents/skills/geniml/.

d="$HOME/.agents/skills/geniml"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/geniml"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/bedspace.md" "$u/references/bedspace.md" \
  -o "$d/references/consensus_peaks.md" "$u/references/consensus_peaks.md" \
  -o "$d/references/region2vec.md" "$u/references/region2vec.md" \
  -o "$d/references/scembed.md" "$u/references/scembed.md" \
  -o "$d/references/utilities.md" "$u/references/utilities.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Antigravity

Neste projeto: instala em .agents/skills/geniml/.

d=".agents/skills/geniml"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/geniml"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/bedspace.md" "$u/references/bedspace.md" \
  -o "$d/references/consensus_peaks.md" "$u/references/consensus_peaks.md" \
  -o "$d/references/region2vec.md" "$u/references/region2vec.md" \
  -o "$d/references/scembed.md" "$u/references/scembed.md" \
  -o "$d/references/utilities.md" "$u/references/utilities.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Global: instala em ~/.gemini/antigravity-cli/skills/geniml/.

d="$HOME/.gemini/antigravity-cli/skills/geniml"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/geniml"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/bedspace.md" "$u/references/bedspace.md" \
  -o "$d/references/consensus_peaks.md" "$u/references/consensus_peaks.md" \
  -o "$d/references/region2vec.md" "$u/references/region2vec.md" \
  -o "$d/references/scembed.md" "$u/references/scembed.md" \
  -o "$d/references/utilities.md" "$u/references/utilities.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Peça ao Rook

Já usa o Rook Labs? Cole no chat do Rook: instale a skill https://rooklabs.sh/marketplace/cct.geniml

Prévia do SKILL.md

---
name: geniml
description: This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for training region embeddings (Region2Vec, BEDspace), single-cell ATAC-seq analysis (scEmbed), building consensus peaks (universes), or any ML-based analysis of genomic regions. Applies to BED fil…
---

# Geniml: Genomic Interval Machine Learning

## Overview

Geniml is a Python package for building machine learning models on genomic interval data from BED files. It provides unsupervised methods for learning embeddings of genomic regions, single cells, and metadata labels, enabling similarity searches, clustering, and downstream ML tasks.

## Installation

Install geniml using uv:

```bash
uv uv pip install geniml
```

For ML dependencies (PyTorch, etc.):

```bash
uv uv pip install 'geniml[ml]'
```

Development version from GitHub:

```bash
uv uv pip install git+https://github.com/databio/geniml.git
```

## Core Capabilities

Geniml provides five primary capabilities, each detailed in dedicated reference files:

### 1. Region2Vec: Genomic Region Embeddings

Train unsupervised embeddings of genomic regions using word2vec-style learning.

**Use for:** Dimensionality reduction of BED files, region similarity analysis, feature vectors for downstream ML.
…

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