packagefinder
seurat
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| packagefinder | seurat | |
|---|---|---|
| 1 | 13 | |
| 43 | 2,118 | |
| - | 3.2% | |
| 0.0 | 9.7 | |
| 6 months ago | 18 days ago | |
| R | R | |
| GNU General Public License v3.0 only | GNU General Public License v3.0 or later |
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.
packagefinder
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R has a lot of good libraries. But what libraries is R missing?
Check out the packagefinder package - I’ve found it to be exactly what I need when looking for packages relevant to specific workflows, etc.
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
What are some alternatives?
scvi-tools - Deep probabilistic analysis of single-cell and spatial omics data
pagoda2 - R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
frontends-team-compass - A repository for team interaction, syncing, and handling meeting notes across the JupyterLab ecosystem.
future - :rocket: R package: future: Unified Parallel and Distributed Processing in R for Everyone
popscle - A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools
MAST - Tools and methods for analysis of single cell assay data in R
osmnx - OSMnx is a Python package to easily download, model, analyze, and visualize street networks and other geospatial features from OpenStreetMap.
ck - Collective Mind (CM) is a simple, modular, cross-platform and decentralized workflow automation framework with a human-friendly interface and reusable automation recipes to make it easier to compose, run, benchmark and optimize AI, ML and other applications and systems across diverse and continuously changing models, data, software and hardware
Peptides - An R package to calculate indices and theoretical physicochemical properties of peptides and protein sequences.