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Seurat Alternatives
Similar projects and alternatives to seurat
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osmnx
OSMnx is a Python package to easily download, model, analyze, and visualize street networks and other geospatial features from OpenStreetMap.
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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 (by mlcommons)
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InfluxDB
Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.
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frontends-team-compass
A repository for team interaction, syncing, and handling meeting notes across the JupyterLab ecosystem.
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pagoda2
R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
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popscle
A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools
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packagefinder
Comfortable search for R packages on CRAN, either directly from the R console or with an R Studio add-in
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Peptides
An R package to calculate indices and theoretical physicochemical properties of peptides and protein sequences.
NOTE:
The number of mentions on this list indicates mentions on common posts plus user suggested alternatives.
Hence, a higher number means a better seurat alternative or higher similarity.
seurat reviews and mentions
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
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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
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A note from our sponsor - SaaSHub
www.saashub.com | 1 May 2024
Stats
Basic seurat repo stats
13
2,125
9.6
21 days ago
satijalab/seurat is an open source project licensed under GNU General Public License v3.0 or later which is an OSI approved license.
The primary programming language of seurat is R.
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