Searches, downloads and analyzes ENCODE Project experiments such as ChIP-seq, ATAC-seq and RNA-seq data; also ships as a Claude Code plugin.
Setup
Choose your client, copy the config, then fill in any required environment variables.
claude mcp add encode-toolkit -- npx -y encode-toolkit~/.codex/config.toml
[mcp_servers.encode-toolkit]
command = "npx"
args = ["-y", "encode-toolkit"]
# codex mcp add encode-toolkit -- npx -y encode-toolkit~/.cursor/mcp.json
{
"mcpServers": {
"encode-toolkit": {
"command": "npx",
"args": [
"-y",
"encode-toolkit"
]
}
}
}.vscode/mcp.json
{
"servers": {
"encode-toolkit": {
"type": "stdio",
"command": "npx",
"args": [
"-y",
"encode-toolkit"
]
}
}
}~/.gemini/settings.json
{
"mcpServers": {
"encode-toolkit": {
"command": "npx",
"args": [
"-y",
"encode-toolkit"
]
}
}
}claude_desktop_config.json
{
"mcpServers": {
"encode-toolkit": {
"command": "npx",
"args": [
"-y",
"encode-toolkit"
]
}
}
}.trae/mcp.json
{
"mcpServers": {
"encode-toolkit": {
"command": "npx",
"args": [
"-y",
"encode-toolkit"
]
}
}
}