Comments (2)
Hi Tomás,
Thank you for your interest in SeuratWrappers! Since this is a community-driven project, we don't have a road map in mind for the future of this package, nor do we have much say in the release schedule. Future versions of this package come at a sporadic rate, even more so than Seurat. Moreover, this package is tied to other R packages hosted on various repositories. Each of these has their own release schedule and none of them are installed when installing SeuratWrappers for the first time. A conda package doesn't make much sense as the dependency structure of this package is too varied.
Furthermore, we fully discourage the use of Conda as it tends to cause a lot of issues, especially with R packages. You can do a quick search of "conda" on the main Seurat repo to get an idea of why we insist that our users use R from CRAN and install our packages using install.packages
or remotes::install_github
(devtools::install_github
is just a reexport of this).
If you're looking for virtual-environments for your R projects, I highly recommend checking out renv
, a virtual-environment and dependency versioneer from RStudio. Since it was built by R people for R people, our code has far fewer issues than with Conda.
from seurat-wrappers.
Hi Paul.
Thank you for your detailed answer. I see your point about the dependencies. In our case, though, all our infrastructure exploits conda to take advantage of its reproducibility features, integration with snakemake, and for the fact that it being largely language-agnostic is key to complex pipelines.
In any case, we can work with a fork and packages in our own repositories. We always like to try to coordinate with the authors and contribute to the community first.
Thanks!
from seurat-wrappers.
Related Issues (20)
- Not able to convert loom to seurat HOT 5
- FastMNNIntegration not using "sketch" assay but "RNA" assay
- Learn_graph error Error: colnames(cds)!=names(cds@clusters[[reduction_method]]$partitions)
- Velocyto- Seurat - invalid class “LogMap” object: Duplicate rownames not allowed HOT 4
- Seurat-wrappers intsallation failure HOT 4
- Bug report(?) of adding support to v5
- negative extents to matrix
- Installing in a Conda environment
- past versions of seurat-wrappers that fits seurat v4 HOT 4
- Warning in install.packages :package ‘SeuratWrappers’ is not available for this version of R HOT 1
- Temporary Files
- Alra not using Scaled data
- Error converting Seurat object to cell_data_set, bug fix no longer exists HOT 1
- IntegrateLayers using FastMNN gives error: 'batch' must be specified if '...' has only one object HOT 2
- Error in .subscript.2ary(x, i, j, drop = TRUE) : subscript out of bounds
- The batch argument for FastMNNIntegration via IntegrateLayers is non-functional
- Warning: Layer counts isn't present in the assay object; returning NULL
- Error: No feature overlap between existing object and new layer data HOT 1
- Unable to open HDF5 file.
- Allow specification of Python virtual environment
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