seurat
frontends-team-compass
| seurat | frontends-team-compass | |
|---|---|---|
| 13 | 3 | |
| 2,129 | 53 | |
| 2.1% | - | |
| 9.6 | 6.9 | |
| 5 days ago | about 2 months ago | |
| R | ||
| GNU General Public License v3.0 or later | BSD 3-clause "New" or "Revised" License |
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.
seurat
- Help with spatial transcriptomic analysis
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Seurat installation issues on macbook (for RNA-seq analysis)
So there is an issue with the ModularityOptimizer? I looked it up and it comes from this script: https://github.com/satijalab/seurat/blob/master/src/RModularityOptimizer.cpp
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Does Seurat provide any advantage for UMAPs over other packages (e.g. uwot)?
With regards to using selected features for UMAP, my gut tells me it's possible, but it looks like the folks here were having some issues getting it work. Your mileage may vary.
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Weird Phishing attempt on GitHub
The strangest thing is that I'm not even a follower of this repo where the discussion was started, which by the way is a R toolkit for single cell genomics.
- I feel like nobody knows anything about what they're doing (including me) and it's making me think twice about working in bioinformatics. Is it a bioinformatics problem or is it a lab problem?
- Use of Seurat integrated assay
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Extract Log-Normalised Data From a Seurat Object
There is a good wiki of the Seurat data object and information about the slots and objects can be found here: https://github.com/satijalab/seurat/wiki
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Reference request: single cell RNA seq papers where cells originate from multiple individuals where the individual of origin was explicitly accounted for in the model?
Here is link number 1 - Previous text "1"
- Seurat
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Is there a way to obtain the raw source codes of Seurat functions?
Wow, it's not easy to find, indeed. They should do a better job commenting the code, and documenting the code organisation. But it's all in the Github repo, for example NormalizeData is defined here: https://github.com/satijalab/seurat/blob/4e868fcde49dc0a3df47f94f5fb54a421bfdf7bc/R/generics.R#L337
frontends-team-compass
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Jupyter + copilot
You may be interested in reading/leaving feedback on https://github.com/jupyterlab/team-compass/issues/172
- Research software code is likely to remain a tangled mess
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I'm working on a tool to help people learn data science with screen readers, so please give me feedback!
On the other hand, it seems that there will be accessibility improvements for Jupyter in the not too distant future. https://github.com/jupyterlab/team-compass/issues/98
What are some alternatives?
scvi-tools - Deep probabilistic analysis of single-cell and spatial omics data
ck - Collective Mind (CM) is a small, modular, cross-platform and decentralized workflow automation framework with a human-friendly interface and reusable automation recipes to make it easier to build, run, benchmark and optimize AI, ML and other applications and systems across diverse and continuously changing models, data, software and hardware
pagoda2 - R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
docker-stacks - Ready-to-run Docker images containing Jupyter applications
future - :rocket: R package: future: Unified Parallel and Distributed Processing in R for Everyone
osmnx - OSMnx is a Python package to easily download, model, analyze, and visualize street networks and other geospatial features from OpenStreetMap.
popscle - A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools
awesome-jupyter - A curated list of awesome Jupyter projects, libraries and resources
MAST - Tools and methods for analysis of single cell assay data in R
JupyterLab - JupyterLab computational environment.
packagefinder - Comfortable search for R packages on CRAN, either directly from the R console or with an R Studio add-in
best-of-jupyter - 🏆 A ranked list of awesome Jupyter Notebook, Hub and Lab projects (extensions, kernels, tools). Updated weekly.