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To validate our results, we used The Cancer Genome Atlas (TCGA) RNA-seq data from the subset of invasive breast carcinomas, which consists of over 500 breast tumor samples. We downloaded the files containing the per-million read count from the TCGA data portal ( -data.nci.nih.gov/tcga/findArchives.htm) and grouped tumors into subtypes according to the Pam50 signature (basal-like, HER2-enriched, luminal A, luminal B, and normal-like; Supplementary Table 4, see section on supplementary data given at the end of this article).
MacPorts is an easy to use system for compiling, installing, and managing open source software. MacPorts may be conceptually divided into two main parts: the infrastructure, known as MacPorts base, and the set of available ports. A MacPorts port is a set of specifications contained in a Portfile that defines an application, its characteristics, and any files or special instructions required to install it. This allows you to use a single command to tell MacPorts to automatically download, compile, and install applications and libraries. But using MacPorts to manage your open source software provides several other significant advantages. For example, MacPorts:
The full distribution filename, including the extract suffix. Used to specify non-default distribution filenames; this keyword must be specified (and tags used) when a port has multiple download files (see master_sites).
The list of dependencies to check before phases fetch, checksum, extract, patch, configure, build, destroot, install, and package. Fetch dependencies are needed to download the distfiles for a port, and are not needed at all once the software is installed.
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