CODEX (CAM)

CODEX software provides a user-friendly database for accessing and analyzing publicly available next-generation sequencing (NGS) data. Specifically designed for experimental biologists, CODEX collects multi-center genomic datasets, processes them uniformly, and vets them for quality. Doing so ensures that the data are directly comparable, irrespective of the publishing laboratory.

The primary aim of CODEX is to provide the scientific community with instant access to high-quality NGS data. This data can be visualized or downloaded immediately, allowing users to compare user-generated data against the database's cumulative knowledge base. The tool contains four types of NGS experiments: transcription factor chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-Seq), histone modification ChIP-Seq, DNase-Seq, and RNA-Seq.

These four types of experiments are largely encompassed within two specialized repositories: HAEMCODE and ESCODE. HAEMCODE is focused on hematopoiesis samples, while ESCODE is focused on embryonic stem cell samples. CODEX has over 1000 samples, including 221 unique TFs and 93 unique cell types. This makes CODEX one of the most complete publicly available NGS data resources.

The tool is particularly useful for scientists interested in directly interrogating transcriptional programs that regulate cellular identity and fate in the context of mammalian development, homeostasis, and disease.