The Metacells.jl package provides computational services for the metacells
package, using Daf to hold the data. In the future, we'll ideally
migrate all of the metacellspackage computations to this package, converting the Python package to a thin wrapper, and
provide a similar thin R wrapper to provide metacell analysis from R as well. For now,Metacells.jl only provides a
subset of the features of the Pythonmetacellspackage, which requires users to convert data fromAnnData(for the old
features) to Daf (to the new features).
See the v0.1.0 documentation for details.
The Python metacells package uses C++ for some of the underlying computations. In addition, higher level computations
are performed directly in Python, with parallelism using multi-processing (based on fork to avoid GIL issues and use
shared memory for at least the inputs). Finally, the current Python metacells is based on the restricted AnnData
format.
This combination of technologies is inefficient (e.g., the use of parallelism is severely restricted, and using GPUs
would require a major overhaul of the code) and awkward (the representation of per-cell, per-metacell, and per-type data
requires a combination of multiple AnnData objects and CSV files). This forced tools like
MCView to implement their own storage mechanism.
To solve these problems, we will be (incrementally) migrating to an implementation where all the computations would be
implemented in Julia using Daf. This would allow us to make the best use of multiple CPUs (and, hopefully, GPUs), and
provide a coherent representation of the data in a single data set, which would allow MCView and similar tools to work
directly from this data set.
For the duration of the transition, we'll maintain the existing metacells implementation to minimize the impact on
existing users. New features will only be available in the new technology stack, and old features will be migrated (one
at a time) to it, until the new system will be complete and the old system will become deprecated.
This process will take a while (months - probably all of 2024), so "Keep calm and carry on" - just use the current
Python metacells package API for now. That said, you would probably want to convert the data from AnnData to Daf
at some point of your processing pipeline, in order to use the new features, and/or use the (updated) MCView tool.
Just Pkg.add("Metacells"), like installing any other Julia package. However, until this package is complete, there's
little point in directly installing it. You should probably install the Python package instead (which will automatically
install the Julia package as a dependency).
To install the Python metacells package, just pip install metacells, like
installing any other Python package.
TODO: To install the R wrappers...
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