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Alevin-fry Alternatives
Similar projects and alternatives to alevin-fry
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pagoda2
R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
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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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SaaSHub
SaaSHub - Software Alternatives and Reviews. SaaSHub helps you find the best software and product alternatives
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mixcr
MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
NOTE:
The number of mentions on this list indicates mentions on common posts plus user suggested alternatives.
Hence, a higher number means a better alevin-fry alternative or higher similarity.
alevin-fry reviews and mentions
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.
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A note from our sponsor - InfluxDB
www.influxdata.com | 2 May 2024
Stats
Basic alevin-fry repo stats
3
149
7.2
about 2 months ago
COMBINE-lab/alevin-fry is an open source project licensed under BSD 3-clause "New" or "Revised" License which is an OSI approved license.
The primary programming language of alevin-fry is Rust.
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