Description
Collection of useful code related to biological analysis. Much of this is
discussed with examples at Blue collar bioinformatics.
Some projects which may be especially interesting:
bccb alternatives and similar packages
Based on the "Science and Data Analysis" category.
Alternatively, view bccb alternatives based on common mentions on social networks and blogs.
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Pandas
Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more -
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Interactive Parallel Computing with IPython
IPython Parallel: Interactive Parallel Computing in Python -
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#<Sawyer::Resource:0x00007f547e829e00>
A unified interface for distributed computing. Fugue executes SQL, Python, Pandas, and Polars code on Spark, Dask and Ray without any rewrites. -
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bcbio-nextgen
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis -
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PatZilla
PatZilla is a modular patent information research platform and data integration toolkit with a modern user interface and access to multiple data sources. -
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cclib
0.9 bccb VS cclibA library for parsing and interpreting the results of computational chemistry packages. -
ElasticBatch
Elasticsearch tool for easily collecting and batch inserting Python data and pandas DataFrames
SaaSHub - Software Alternatives and Reviews
* Code Quality Rankings and insights are calculated and provided by Lumnify.
They vary from L1 to L5 with "L5" being the highest.
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README
Collection of useful code related to biological analysis. Much of this is discussed with examples at Blue collar bioinformatics.
All code, images and documents in this repository are freely available for all uses. Code is available under the MIT license and images, documentations and talks under the Creative Commons No Rights Reserved (CC0) license.
Some projects which may be especially interesting:
- CloudBioLinux -- An automated environment to install useful biological software and libraries. This is used to bootstrap blank machines, such as those you'd find on Cloud providers like Amazon, to ready to go analysis workstations. See the CloudBioLinux effort for more details. This project moved to its own repository at https://github.com/chapmanb/cloudbiolinux.
- gff -- A GFF parsing library in Python, aimed for inclusion into Biopython.
- nextgen -- A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis. This project has moved into its own repository: https://github.com/chapmanb/bcbio-nextgen
- distblast -- A distributed BLAST analysis running for identifying best hits in a wide variety of organisms for downstream phylogenetic analyses. The code is generalized to run on local multi-processor and distributed Hadoop clusters.
*Note that all licence references and agreements mentioned in the bccb README section above
are relevant to that project's source code only.