frontends-team-compass
A repository for team interaction, syncing, and handling meeting notes across the JupyterLab ecosystem. (by jupyterlab)
seurat
R toolkit for single cell genomics (by satijalab)
| frontends-team-compass | seurat | |
|---|---|---|
| 3 | 13 | |
| 53 | 2,129 | |
| - | 2.1% | |
| 6.9 | 9.6 | |
| 2 months ago | 6 days ago | |
| R | ||
| BSD 3-clause "New" or "Revised" License | GNU General Public License v3.0 or later |
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.
frontends-team-compass
Posts with mentions or reviews of frontends-team-compass.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2021-02-22.
-
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
-
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
seurat
Posts with mentions or reviews of seurat.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-02-06.
- Help with spatial transcriptomic analysis
-
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
-
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.
-
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
-
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
-
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
-
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?
When comparing frontends-team-compass and seurat you can also consider the following projects:
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
scvi-tools - Deep probabilistic analysis of single-cell and spatial omics data
docker-stacks - Ready-to-run Docker images containing Jupyter applications
pagoda2 - R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
osmnx - OSMnx is a Python package to easily download, model, analyze, and visualize street networks and other geospatial features from OpenStreetMap.
future - :rocket: R package: future: Unified Parallel and Distributed Processing in R for Everyone