pagoda2
R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets (by kharchenkolab)
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. (by COMBINE-lab)
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pagoda2 | alevin-fry | |
---|---|---|
2 | 3 | |
191 | 149 | |
2.1% | 2.7% | |
5.3 | 7.2 | |
2 months ago | about 2 months ago | |
JavaScript | Rust | |
- | BSD 3-clause "New" or "Revised" License |
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.
pagoda2
Posts with mentions or reviews of pagoda2.
We have used some of these posts to build our list of alternatives
and similar projects.
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GOterm analysis in Seurat
Try pagoda2 for this: https://github.com/kharchenkolab/pagoda2
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Seurat Vs Pagoda2 For Scrnaseq Analysis
I realize that this is a bit old, but I find pagoda2 faster: https://github.com/kharchenkolab/pagoda2
alevin-fry
Posts with mentions or reviews of alevin-fry.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-12-01.
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RNA VELOCITY
You can also get this information easily from the raw data using our alevin-fry tool. It produces a count matrix with spliced/unspliced/ambiguous counts that can easily be imported into python or R for velocity analysis. You can read more about alevin-fry here and check it out on github here. It's also easily installable via bioconda, and there's even a tool to simplify execution, called simpleaf. I'm happy to answer any questions you might have about using it!
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"Surpassing" Go & the near-future of Rust: in what domains will Rust succeed?
I think it depends on where in the space one is working. Our most recent tool, for example, is alevin-fry, which is for efficient preprocessing of single cell RNA seq data. Rust is the natural replacement for tools in the space that otherwise would have been in C++ (aligners, assemblers, large scale indexing, and things like RNA seq quantification and preprocessing). I view julia as more appropriate to replace tools currently existing in Python or R. There, I believe it can offer some substantial benefits. For our applications however, garbage collection is usually a non-starter.
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Our lab did a thing in rust (single-cell bioinformatics)
My lab has been trying to move most of our development over to rust (from C++). Our most recent paper presents a tool for single-cell and single-nucleus RNA-seq processing in rust https://rdcu.be/cIL35. The repo is https://github.com/COMBINE-lab/alevin-fry. It's one of our first "big" rust packages; so hopefully our design practices and rust skills will continue to improve.
What are some alternatives?
When comparing pagoda2 and alevin-fry you can also consider the following projects:
seurat - R toolkit for single cell genomics
rust - Empowering everyone to build reliable and efficient software.
scanpy - Single-cell analysis in Python. Scales to >1M cells.
deno - A modern runtime for JavaScript and TypeScript.
kana - Single cell analysis in the browser
AreWeRustYet - Awesome list of "Are We *thing* Yet" for Rust
too-many-cells - Cluster single cells and analyze cell clade relationships with colorful visualizations.
alacritty - A cross-platform, OpenGL terminal emulator.
mirdeep2 - Discovering known and novel miRNAs from small RNA sequencing data
mixcr - MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.