Everyome

Every -ome, for everyone.

Created by Helen R Horkan PhD (Stowers Institute). If you use Everyome, adapt its code, or reuse its text or figures, please cite it (see CITATION.cff).

Everyome is a free, open-source platform for omics analysis. It gives biologists a simple point-and-click interface while keeping every setting visible and editable. It runs on your own computer or on your own Slurm cluster account over SSH, so your data stays where it is.

Planned suites: DNA, RNA, single cell, spatial, protein, molecular biology and phylogenetics. Every module will come with a manual, a playground, guides to reading its output, and a lab-book protocol and methods section for every run.

Everyome grows out of SPLiTscape (SPLiT-seq reads to annotated cell atlases), which becomes its first single-cell module and keeps its own citation.

Status

The core is in place (phase 1 of docs/PLAN.md): connect to a cluster or the built-in demo cluster, create projects, choose an analysis, fill in its settings, check the exact job scripts, submit them, follow the jobs, and explore the results in a live session. Every run then gets a lab-book protocol, a draft methods section to edit, its references, and a bundle that repeats it exactly.

Modules so far:

• SPLiT-seq (SPLiTscape), single cell: SPLiT-seq sublibraries from raw reads to annotated cell types, on their own (for example, to build a first atlas) or merged with an existing atlas or dataset. Includes a playground.
• Bulk RNA-seq differential expression, RNA: nf-core/rnaseq turns reads into gene counts on the cluster, then DESeq2 compares conditions in a live session.
• Sequence summary, getting started: a small worked example of how every module runs.

Install

pip install "everyome==0.1.0a1"          # the app and the tutorial
pip install "everyome[all]==0.1.0a1"     # plus SPLiT-seq and bulk RNA-seq (Scanpy, PyDESeq2, ...)
everyome                              # opens http://127.0.0.1:8777

Naming the version installs this early release of Everyome while everything it needs comes from normal, stable releases. (Avoid pip install --pre: it would also pull in unfinished versions of other packages.) Everyome needs Python 3.10 or newer and runs on macOS and Linux. Choose Demo cluster to try everything on your own computer, with example data and a pretend job scheduler; demo data lives in ~/.everyome/demo_cluster (delete it to start fresh). To use your own cluster, Everyome also needs to be installed in a Python environment there (ask IT for a shared one), and the readiness checks tell you what is missing.

Develop

git clone https://github.com/Everyome/everyome && cd everyome
pip install -e ".[test,all]"
pytest

Licence

MIT (see LICENSE). Fonts, UMAP-JS and the nf-core/rnaseq schemas that ship with Everyome keep their own licences; see THIRD_PARTY_NOTICES.md.