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Sage Alternatives
Similar projects and alternatives to sage
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rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
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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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Rust-Bio
This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.
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gatk4-genome-processing-pipeline-azure
Workflows used for processing whole genome sequence data + germline variant calling.
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NOTE:
The number of mentions on this list indicates mentions on common posts plus user suggested alternatives.
Hence, a higher number means a better sage alternative or higher similarity.
sage reviews and mentions
Posts with mentions or reviews of sage.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-06-06.
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Does anyone know a great guide/documentation explaining how to implement Percolator?
If you want to implement LDA from scratch, you could check out how Sage is doing it.
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What are some good examples of well-engineered bioinformatics pipelines?
You could check out https://github.com/lazear/sage - it's a near comprehensive program/pipeline for analyzing DDA/shotgun proteomics data. Most proteomics pipelines consist of running multiple, separate tools in sequence (search, spectrum rescoring, retention time prediction, quantification), but sage performs all of these. This cuts down on the need for disk space for storing intermediate results (none required), the need for IO (files are read once), and results in a proteomics pipeline that is >10-1000x faster than anything else, including commercial solutions
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Proteomics search engine written in Rust
You can also check out the intro blog post if you're interesting in learning more about the algorithm behind Sage. Beyond being fast, it also includes integrated machine learning (linear discriminant analysis, KDE) for rescoring spectral matches.
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Opinions on AlphaPept
You could try out Sage, if you're looking for speed - I don't think you'll find anything faster. https://github.com/lazear/sage
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Stats
Basic sage repo stats
5
188
7.7
17 days ago
lazear/sage is an open source project licensed under MIT License which is an OSI approved license.
The primary programming language of sage is Rust.
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