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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statsmodels
Statsmodels: statistical modeling and econometrics in Python -
PyMC
Probabilistic Programming in Python: Bayesian Modeling and Probabilistic Machine Learning with Aesara -
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Biopython
Official git repository for Biopython (originally converted from CVS) -
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Interactive Parallel Computing with IPython
Interactive Parallel Computing in Python -
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Cubes
Light-weight Python OLAP framework for multi-dimensional data analysis -
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bcbio-nextgen
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis -
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Neupy
NeuPy is a Tensorflow based python library for prototyping and building neural networks -
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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. -
Kotori
A flexible data historian based on InfluxDB, Grafana, MQTT and more. Free, open, simple. -
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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 -
dask-memusage
A low-impact profiler to figure out how much memory each task in Dask is using -
Open Babel
A chemical toolbox designed to speak the many languages of chemical data.
Scout APM - Leading-edge performance monitoring starting at $39/month
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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.