Scikit-bio Alternatives

Similar projects and alternatives to scikit-bio

Primes

45 2,363 7.0 C# scikit-bio VS Primes

Prime Number Projects in C#/C++/Python
benchmarks

40 2,747 7.2 Makefile scikit-bio VS benchmarks

Some benchmarks of different languages
InfluxDB

www.influxdata.com featured

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.
nimpy

38 1,420 5.8 Nim scikit-bio VS nimpy

Nim - Python bridge
Arraymancer

21 1,309 8.2 Nim scikit-bio VS Arraymancer

A fast, ergonomic and portable tensor library in Nim with a deep learning focus for CPU, GPU and embedded devices via OpenMP, Cuda and OpenCL backends
PrimesResult

6 28 0.0 scikit-bio VS PrimesResult

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RecursiveFactorization.jl

8 74 6.1 Julia scikit-bio VS RecursiveFactorization.jl
nimtorch

3 452 10.0 Nim scikit-bio VS nimtorch

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SaaSHub

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nimpylib

1 183 3.4 Nim scikit-bio VS nimpylib

Some python standard library functions ported to Nim
biofast

3 175 0.0 C scikit-bio VS biofast

Benchmarking programming languages/implementations for common tasks in Bioinformatics
viroiddb

2 5 0.0 Vue scikit-bio VS viroiddb

A curated database of all available viroid-like RNA 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 scikit-bio alternative or higher similarity.

Suggest an alternative to scikit-bio

scikit-bio reviews and mentions

Posts with mentions or reviews of scikit-bio. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2021-09-23.

What are some of the bioinformatic projects I could do on python as a beginner?
1 project | /r/pythontips | 12 Jul 2023
Why I Use Nim instead of Python for Data Processing
12 projects | news.ycombinator.com | 23 Sep 2021

You make a fair point that using optimized numerical libraries instead of string methods will be ridiculously fast because they're compiled anyway. For example, scikit-bio does just this for their reverse complement operation [1]. However, they use an 8 bit representation since they need to be able to represent the extended IUPAC notation for ambiguous bases, which includes things like the character N for "aNy" nucleotide [2]. One could get creative with a 4 bit encoding and still end up saving space (assuming you don't care about the distinction between upper versus lowercase characters in your sequence [2]). Or, if you know in advance your sequence is unambiguous (unlikely in DNA sequencing-derived data) you could use the 2 bit encoding. When dealing with short nucleotide sequences, another approach is to encode the sequence as an integer. I would love to see a library—Python, Nim, or otherwise—that made using the most efficient encoding for a sequence transparent to the developer.
[1] https://github.com/biocore/scikit-bio/blob/b470a55a8dfd054ae...
[2] https://en.wikipedia.org/wiki/Nucleic_acid_notation
[3]