seurat
popscle
| seurat | popscle | |
|---|---|---|
| 13 | 1 | |
| 2,129 | 43 | |
| 2.1% | - | |
| 9.6 | 2.7 | |
| 5 days ago | about 3 years ago | |
| R | C++ | |
| GNU General Public License v3.0 or later | Apache License 2.0 |
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
popscle
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Genotype single cell data?
You can get vcf files from 10x bam files with freemuxlet. ATAC-seq or RNA-seq.
What are some alternatives?
scvi-tools - Deep probabilistic analysis of single-cell and spatial omics data
scCODA - A Bayesian model for compositional single-cell data analysis
pagoda2 - R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
cellsnp-lite - Efficient genotyping bi-allelic SNPs on single cells
frontends-team-compass - A repository for team interaction, syncing, and handling meeting notes across the JupyterLab ecosystem.
rnaseqc - Fast, efficient RNA-Seq metrics for quality control and process optimization
future - :rocket: R package: future: Unified Parallel and Distributed Processing in R for Everyone
MAST - Tools and methods for analysis of single cell assay data in R
packagefinder - Comfortable search for R packages on CRAN, either directly from the R console or with an R Studio add-in
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 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
Peptides - An R package to calculate indices and theoretical physicochemical properties of peptides and protein sequences.