GitHub

Dynema.jl

See our pre-print using this link

Dynema (Dynamic eQTL mapping in single cells) is a fast and calibrated method to map eQTL effects genome-wide at true single-cell resolution. We argue that an eQTL effect is different for each individual cell. Dynema can decompose such effects into: i) context-independent (main), ii) context-dependent (interaction), and iii) total (main and interaction).

No Julia coding required: Dynema ships a command-line interface that runs the full mapping workflow – straight from a VCF and a Matrix Market count matrix to per-gene summary statistics tables, in batches of genes ready to parallelize on any HPC scheduler – entirely from the terminal. See the Command-line overview to get started. A Julia API is also available for anyone who wants to call Dynema directly from their own scripts or pipelines – see the API Reference.

Getting started

  • Quick start (end to end) from input files (VCF + Matrix Market expression) through data indexing, and single-cell eQTL tests on a small simulated dataset.
  • Command-line overview familiarizes with running Dynema and its parameters from a VCF and a Matrix Market count matrix, without writing any Julia code.
  • API Reference documents every exported function, for anyone calling Dynema directly from Julia.

Getting help

Please open an issue on GitHub for bug reports or feature requests. Feedback is also very welcomed!