Atom runs as a Web app in Electron (formerly atom-shell), which is basically a stripped-down version of the Chromium browser combined with Node.js and some additions to ease interop between the Web app and the host OS.
Npm uses Web protocols (HTTP, maybe JSON-RPC) to communicate with repository servers.
This is not saying that there aren't any non-web applications using Node.js, just that web-related applications using Node.js are quite numerous and popular.
Personally I know of Node.js applications and libraries targeting robotics, computer vision, language analysis, neural networks and more. Like any powerful platform, much of this relies on the ability of Node.js to interface with external libraries, which it does using wrappers built with node-gyp.
Npm uses Web protocols (HTTP, maybe JSON-RPC) to communicate with repository servers.
This is not saying that there aren't any non-web applications using Node.js, just that web-related applications using Node.js are quite numerous and popular.
Personally I know of Node.js applications and libraries targeting robotics, computer vision, language analysis, neural networks and more. Like any powerful platform, much of this relies on the ability of Node.js to interface with external libraries, which it does using wrappers built with node-gyp.