workflowr
Organize your project into a research website (by workflowr)
data-science-development-project-template
A logical, reasonably standardized, but flexible project structure for doing and sharing data science research work while developing a software tool. (by michael-ford)
workflowr | data-science-development-project-template | |
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2 | 1 | |
807 | 4 | |
0.9% | - | |
5.4 | 5.4 | |
2 months ago | 28 days ago | |
R | Jupyter Notebook | |
GNU General Public License v3.0 or later | MIT License |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
workflowr
Posts with mentions or reviews of workflowr.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-11-17.
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How do you manage results, plots, etc.?
I would start by saying "bioinformatics world" is a very broad term. Most of it does not involve managing multiple models, which is what MLflow seems to be for. Most work is cleaning the data and interpreting the results, which is highly project-specific. Something like workflowr is generally more appropriate, but even that is an overkill for most people.
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Restructuring a large R project. Need advice on how to wire up file paths and associated objects.
Targets stores all your data serialised on disk, and only loads them in as needed by the dependencies. For a standardised folder structure, you can take inspiration from workflowr.
data-science-development-project-template
Posts with mentions or reviews of data-science-development-project-template.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-11-17.
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How do you manage results, plots, etc.?
Bioinf has a lot of biologists who have transitioned into more technical/coding focused roles, so you'll find there's not a lot of engineering workflow standards out there compared to DS or SWE. As others have said, snakemake is the most common, but thats just a pipeline managment tool, it doesn't manage data or outputs. I personally use DVC for data and pipeline management (and include jupyter and papermill to make it all work), although I haven't yet gotten onboard with their experiments feature (which is what would manage different parameters and figures/results beyond versioning). I looked into MLflow and some other options when I was getting started (I do tool development and bioinf analysis), but I wanted data versioning to ensure experiment reproducibility (kind of a critcal part of science IMO), and many of the other solutions like Airflow (common in DS industry) seemed to be overkill for smaller bioinfo projects. DVC meets the requirements and I like it in concept, although in practice there have been many updates that have been a bit of a pain to keep up with/integrate. I've got a bioinfo/ds project template on github that roles together git, conda, DVC, jupyter and papermill to ensure experiment reproducibility, and is setup as a template that can be deployed with cookiecutter - check it out if you like.
What are some alternatives?
When comparing workflowr and data-science-development-project-template you can also consider the following projects:
targets - Function-oriented Make-like declarative workflows for R
box - Write reusable, composable and modular R code
targets-minimal - A minimal example data analysis project with the targets R package
reprex - Render bits of R code for sharing, e.g., on GitHub or StackOverflow.
blogdown - Create Blogs and Websites with R Markdown
webR-quarto-demos - Experiments with generating a standalone Quarto Document using Web R
namer - R package :package: for labelling chunks of RMarkdown files! :boom: