pagoda2 vs seurat

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pagoda2		seurat
	Project
2	Mentions	13
191	Stars	2,118
5.8%	Growth	3.2%
5.3	Activity	9.7
2 months ago	Latest Commit	18 days ago
JavaScript	Language	R
-	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.

pagoda2

Posts with mentions or reviews of pagoda2. We have used some of these posts to build our list of alternatives and similar projects.

GOterm analysis in Seurat
1 project | /r/bioinformatics | 6 Aug 2022

Try pagoda2 for this: https://github.com/kharchenkolab/pagoda2
Seurat Vs Pagoda2 For Scrnaseq Analysis
1 project | /r/bioinformatics | 4 Jan 2021

I realize that this is a bit old, but I find pagoda2 faster: https://github.com/kharchenkolab/pagoda2

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
1 project | /r/bioinformatics | 9 Dec 2023
Seurat installation issues on macbook (for RNA-seq analysis)
1 project | /r/bioinformatics | 7 Dec 2023

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)?
1 project | /r/bioinformatics | 8 Mar 2023

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
1 project | dev.to | 29 Dec 2022

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?
1 project | /r/bioinformatics | 7 Dec 2022
Use of Seurat integrated assay
2 projects | /r/bioinformatics | 6 Feb 2022
Extract Log-Normalised Data From a Seurat Object
1 project | /r/bioinformatics | 6 Feb 2022

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?
5 projects | /r/bioinformatics | 2 Feb 2022

Here is link number 1 - Previous text "1"
Seurat
1 project | /r/rprogramming | 11 Jul 2021
Is there a way to obtain the raw source codes of Seurat functions?
1 project | /r/bioinformatics | 22 May 2021

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 pagoda2 and seurat you can also consider the following projects:

scanpy - Single-cell analysis in Python. Scales to >1M cells.

scvi-tools - Deep probabilistic analysis of single-cell and spatial omics data

kana - Single cell analysis in the browser

frontends-team-compass - A repository for team interaction, syncing, and handling meeting notes across the JupyterLab ecosystem.

alevin-fry - 🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

future - :rocket: R package: future: Unified Parallel and Distributed Processing in R for Everyone

too-many-cells - Cluster single cells and analyze cell clade relationships with colorful visualizations.

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

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 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