apm is Atom's native package manager. It allows the user to manage packages and themes without having to initialise Atom itself.
apm comes with the official installation and is automatically added to
%PATH% if you're on Windows.
apm, go to Command Prompt and type
$ apm <command>
Here is the list of what you can do with this package manager.
clean, config, dedupe, deinstall, delete, dev, develop, disable, docs, enable, erase, featured, home, i, init, install, link, linked, links, list, ln, lns, login, ls, open, outdated, publish, rebuild, rebuild-module-cache, remove, rm, search, show, star, starred, stars, test, uninstall, unlink, unpublish, unstar, update, upgrade, view.
For example, if you want to do upgrade all packages from atom:
apm upgrade --confirm false
Or if you want to install a specific package:
apm install <package_name>